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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 51 Structures.

Refinements

Structure Determination Methodology

experimental (51)

Scientific Name of Source Organism

	Homo sapiens (16)
	synthetic construct (14)
	Escherichia coli K-12 (5)
	Podisus maculiventris (5)
	Clostridium botulinum (2)
	Gallus gallus (2)
	Human immunodeficiency virus type 1 group M subtype B (isolate BRVA) (2)
	Paenibacillus polymyxa (2)
	Paenibacillus sp. Y412MC10 (2)
	Acinetobacter baumannii (1)

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Taxonomy

	Eukaryota (22)
	Bacteria (21)
	other sequences (14)
	Eukaryota (eukaryotes) (2)
	Riboviria (RNA viruses and viroids) (2)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (34)
	SOLUTION NMR (14)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

	Protein (51)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (12)
	2.0 - 2.5 (6)
	2.5 - 3.0 (6)
	3.0 - 3.5 (6)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (1)
	2000 - 2004 (4)
	2005 - 2009 (5)
	2010 - 2014 (4)
	2015 - 2019 (13)
	2020 - 2024 (23)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (10)
	Transferases (9)
	Oxidoreductases (2)
	Lyases (1)

Membrane Protein Annotation

	PDBTM (5)
	OPM (4)
	MemProtMD (4)
	mpstruc (2)

Symmetry Type

	Asymmetric (44)
	Cyclic (6)
	Dihedral (4)

SCOP Classification

	Alpha and beta proteins (a/b) (2)
	Small proteins (2)
	Alpha and beta proteins (a+b) (3)
	Peptides (2)

AllSelected

1 to 25 of 51 Structures

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1B4H \| pdb_00001b4h	Download File View File

OLIGO-PEPTIDE BINDING PROTEIN COMPLEXED WITH LYSYL-DIAMINOBUTYRIC ACID-LYSINE

Davies, T.G., Tame, J.R.H.

(1999) Protein Sci 8: 1432-1444

Released	1998-11-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	LYS-DAB-LYS PEPTIDE (protein) PERIPLASMIC OLIGO-PEPTIDE BINDING PROTEIN (protein)
Unique Ligands	U1

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1J73 \| pdb_00001j73	Download File View File

Crystal structure of an unstable insulin analog with native activity.

Wan, Z., Zhao, M., Nakagawa, S., Jia, W., Weiss, M.A.

(2002) J Mol Biology 315: 103-111

Released	2001-05-30
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	insulin a (protein) insulin b (protein)
Unique Ligands	ZN

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1J9V \| pdb_00001j9v	Download File View File

Solution structure of a lactam analogue (DabD) of HIV gp41 600-612 loop.

Phan Chan Du, A., Limal, D., Semetey, V., Dali, H., Jolivet, M., Desgranges, C., Cung, M.T., Briand, J.P., Petit, M.C., Muller, S.

(2002) J Mol Biology 323: 503-521

Released	2003-07-01
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus type 1 group M subtype B (isolate BRVA)
Macromolecule	DabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41 (protein)

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1JAR \| pdb_00001jar	Download File View File

Solution structure of lactam analogue (DDab)of HIV gp41 600-612 loop.

Phan Chan Du, A., Limal, D., Semetey, V., Dali, H., Jolivet, M., Desgranges, C., Cung, M.T., Briand, J.P., Petit, M.C., Muller, S.

(2002) J Mol Biology 323: 503-521

Released	2003-07-01
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus type 1 group M subtype B (isolate BRVA)
Macromolecule	DDab: (ACE)IWGDSGKLI(DAB)TTA ANALOGUE OF HIV GP41 (protein)

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1JDK \| pdb_00001jdk	Download File View File

solution structure of lactam analogue (EDap) of HIV gp41 600-612 loop.

Phan Chan Du, A., Limal, D., Semetey, V., Dali, H., Jolivet, M., Desgranges, C., Cung, M.T., Briand, J.P., Petit, M.C., Muller, S.

(2002) J Mol Biology 323: 503-521

Released	2003-07-01
Method	SOLUTION NMR
Macromolecule	ACETYL GROUP (protein)

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2M7I \| pdb_00002m7i	Download File View File

Solution structure of a Beta-Hairpin Peptidomimetic antibiotic that targets LptD in Pseudomonas sp.

Moehle, K., Schmidt, J., Robinson, J.

(2013) Bioorg Med Chem 21: 5806-5810

Released	2013-09-11
Method	SOLUTION NMR
Macromolecule	Beta-Hairpin Peptidomimetic antibiotic TWL(DAB)(ORN)(DLY)RW(ORN)(DAB)AK(DPR)P (protein)

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2N5W \| pdb_00002n5w	Download File View File

The NMR solution structure of octyl-tridecaptin A1 in DPC micelles

Cochrane, S.A., Findlay, B., Bakhtiary, A., Acedo, J.Z., Rodriguez-Lopez, E.M., Vederas, J.C.

(2016) Proc Natl Acad Sci U S A 113: 11561-11566

Released	2016-09-28
Method	SOLUTION NMR
Macromolecule	Octyl-tridecaptin A1 (protein)

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2N5Y \| pdb_00002n5y	Download File View File

Solution NMR structure of octyl-tridecaptin A1 in DPC micelles containing Gram-negative lipid II

Cochrane, S.A., Findlay, B., Bakhtiary, A., Rodriguez-Lopez, E.M., Vederas, J.C.

(2016) Proc Natl Acad Sci U S A 113: 11561-11566

Released	2016-09-28
Method	SOLUTION NMR
Macromolecule	Octyl-tridecaptin A1 (protein)

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2PM1 \| pdb_00002pm1	Download File View File

Derivative of human alpha-defensin 1 (HNP1)

Lubkowski, J., Pazgier, M., Lu, W.

To be published

Released	2007-05-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1) (protein)

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2W76 \| pdb_00002w76	Download File View File

Structures of P. aeruginosa FpvA bound to heterologous pyoverdines: FpvA-Pvd(Pa6)-Fe complex

Greenwald, J., Nader, M., Celia, H., Gruffaz, C., Meyer, J.-M., Schalk, I.J., Pattus, F.

(2009) Mol Microbiol 72: 1246

Released	2009-05-12
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	FERRIPYOVERDINE RECEPTOR (protein) PYOVERDIN R (protein)
Unique Ligands	FE, N8E, PO4, PVE

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3D3S \| pdb_00003d3s	Download File View File

Crystal structure of L-2,4-diaminobutyric acid acetyltransferase from Bordetella parapertussis

Kim, Y., Volkart, L., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2008-07-15
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Bordetella parapertussis 12822
Macromolecule	L-2,4-diaminobutyric acid acetyltransferase (protein)
Unique Ligands	DAB, GOL, SO4

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3DS9 \| pdb_00003ds9	Download File View File

A potent peptidomimetic inhibitor of botulinum neurotoxin serotype A has a very different conformation than SNAP-25 substrate

Zuniga, J.E., Fenn, T.

(2008) Structure 16: 1588-1597

Released	2008-09-30
Method	X-RAY DIFFRACTION 1.758 Å
Organisms	Clostridium botulinum
Macromolecule	Botulinum neurotoxin type A (protein) octapeptide I1 inhibitor (protein)
Unique Ligands	NI, ZN

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3FQ9 \| pdb_00003fq9	Download File View File

Design of an insulin analog with enhanced receptor-binding selectivity. Rationale, structure, and therapeutic implications

Zhao, M., Wan, Z.L., Whittaker, L., Xu, B., Phillips, N., Katsoyannis, P., Whittaker, J., Weiss, M.A.

(2009) J Biological Chem 284: 32178-32187

Released	2009-08-04
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Homo sapiens
Macromolecule	Insulin (protein)
Unique Ligands	ZN

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3KED \| pdb_00003ked	Download File View File

Crystal structure of Aminopeptidase N in complex with 2,4-diaminobutyric acid

Addlagatta, A., Gumpena, R.

(2011) ChemMedChem 6: 1971-1976

Released	2010-11-03
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli K-12
Macromolecule	Aminopeptidase N (protein)
Unique Ligands	DAB, GOL, MLA, NA, ZN

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3U4W \| pdb_00003u4w	Download File View File

Src in complex with DNA-templated macrocyclic inhibitor MC4b

Seeliger, M.A., Liu, D.R., Georghiou, G., Kleiner, R.E., Pulkoski-Gross, M.

(2012) Nat Chem Biol 8: 366-374

Released	2012-02-22
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Gallus gallus
Macromolecule	Proto-oncogene tyrosine-protein kinase Src (protein) macrocyclic inhibitor MC4B (protein)
Unique Ligands	GOL, SO4

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3U51 \| pdb_00003u51	Download File View File

Src in complex with DNA-templated macrocyclic inhibitor MC1

Seeliger, M.A., Liu, D.R., Georghiou, G., Kleiner, R.E., Pulkoski-Gross, M.

(2012) Nat Chem Biol 8: 366-374

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.241 Å
Organisms	Gallus gallus
Macromolecule	Proto-oncogene tyrosine-protein kinase Src (protein) macrocyclic inhibitor MC1 (protein)

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4XMZ \| pdb_00004xmz	Download File View File

Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with 2,4-diaminobutyric acid

Addlagatta, A., Gumpena, R.

To be published

Released	2016-01-27
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Escherichia coli K-12
Macromolecule	Aminopeptidase N (protein)
Unique Ligands	DAB, GOL, NA, ZN

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4ZJX \| pdb_00004zjx	Download File View File

Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with a Novel Cyclic Peptide Inhibitor

Kumaran, D., Swaminathan, S.

To be published

Released	2016-06-01
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Clostridium botulinum synthetic construct
Macromolecule	Botulinum neurotoxin type A (protein) circular peptide inhibitor (protein)
Unique Ligands	SO4, ZN

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5L3F \| pdb_00005l3f	Download File View File

LSD1-CoREST1 in complex with polymyxin B

Speranzini, V., Rotili, D., Ciossani, G., Pilotto, S., Forgione, M., Lucidi, A., Forneris, F., Velankar, S., Mai, A., Mattevi, A.

(2016) Sci Adv 2: e1601017-e1601017

Released	2016-09-21
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Homo sapiens Paenibacillus polymyxa
Macromolecule	Lysine-specific histone demethylase 1A (protein) Polmyxin B (protein) REST corepressor 1 (protein)
Unique Ligands	FAD

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5L3G \| pdb_00005l3g	Download File View File

LSD1-CoREST1 in complex with polymyxin E (colistin)

Speranzini, V., Rotili, D., Ciossani, G., Pilotto, S., Forgione, M., Lucidi, A., Forneris, F., Velankar, S., Mai, A., Mattevi, A.

(2016) Sci Adv 2: e1601017-e1601017

Released	2016-09-21
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens Paenibacillus polymyxa
Macromolecule	Lysine-specific histone demethylase 1A (protein) REST corepressor 1 (protein) polymyxin E (protein)
Unique Ligands	FAD, NA

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5LRV \| pdb_00005lrv	Download File View File

Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin

Mevissen, T.E.T., Kulathu, Y., Mulder, M.P.C., Geurink, P.P., Maslen, S.L., Gersch, M., Elliott, P.R., Burke, J.E., van Tol, B.D.M., Akutsu, M., El Oualid, F., Kawasaki, M., Freund, S.M.V., Ovaa, H., Komander, D.

(2016) Nature 538: 402-405

Released	2016-10-19
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	OTU domain-containing protein 7B (protein) Polyubiquitin-B (protein)
Unique Ligands	GOL, PO4

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5YU4 \| pdb_00005yu4	Download File View File

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

Min, K.J., Yoon, H.J., Matsuura, A., Kim, Y.H., Lee, H.H.

(2018) Mol Cells 41: 331-341

Released	2018-05-02
Method	X-RAY DIFFRACTION 2.144 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	DAB, NA, NAD

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6CBI \| pdb_00006cbi	Download File View File

PCNA in complex with inhibitor

Bruning, J.B., Wegener, K.L.

(2018) Chemistry 24: 11325-11331

Released	2018-07-04
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Homo sapiens
Macromolecule	GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS (protein) Proliferating cell nuclear antigen (protein)
Unique Ligands	SO4

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6CIV \| pdb_00006civ	Download File View File

Lactam cyclised mimetic of a fragment of p21

Wegener, K.L.

(2018) Chemistry 24: 11325-11331

Released	2018-07-04
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	p21 (protein)

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6D2U \| pdb_00006d2u	Download File View File

Solution structure of a ultra-high affinity macrocycle bound to HIV-1 TAR RNA

Shortridge, M.D., Varani, G.

(2019) Nucleic Acids Res 47: 1523-1531

Released	2018-12-12
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO (protein) RNA (29-MER) (nucleic acid)

1 to 25 of 51 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1B4H | pdb_00001b4h

1J73 | pdb_00001j73

1J9V | pdb_00001j9v

1JAR | pdb_00001jar

1JDK | pdb_00001jdk

2M7I | pdb_00002m7i

2N5W | pdb_00002n5w

2N5Y | pdb_00002n5y

2PM1 | pdb_00002pm1

2W76 | pdb_00002w76

3D3S | pdb_00003d3s

3DS9 | pdb_00003ds9

3FQ9 | pdb_00003fq9

3KED | pdb_00003ked

3U4W | pdb_00003u4w

3U51 | pdb_00003u51

4XMZ | pdb_00004xmz

4ZJX | pdb_00004zjx

5L3F | pdb_00005l3f

5L3G | pdb_00005l3g

5LRV | pdb_00005lrv

5YU4 | pdb_00005yu4

6CBI | pdb_00006cbi

6CIV | pdb_00006civ

6D2U | pdb_00006d2u