3BIU

Human thrombin-in complex with UB-THR10

PDB DOI: https://doi.org/10.2210/pdb3BIU/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, Hirudo medicinalis
Mutation(s): No

Deposited: 2007-12-01 Released: 2007-12-25
Deposition Author(s): Gerlach, C., Smolinski, M., Steuber, H., Sotriffer, C.A., Heine, A., Hangauer, D.G., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.263
R-Value Work: 0.164
R-Value Observed: 0.164

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Thermodynamic Inhibition Profile of a Cyclopentyl and a Cyclohexyl Derivative towards Thrombin: The Same but for Different Reasons

Gerlach, C., Smolinski, M., Steuber, H., Sotriffer, C.A., Heine, A., Hangauer, D.G., Klebe, G.

(2007) Angew Chem Int Ed Engl 46: 8511-8514

PubMed: 17902081 Search on PubMed
DOI: https://doi.org/10.1002/anie.200701169
Primary Citation of Related Structures:
3BIU, 3BIV

Organizational Affiliation

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 35.2 kDa
Atom Count: 2,552
Modelled Residue Count: 288
Deposited Residue Count: 298
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A [auth L]	29	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	B [auth H]	257	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth H]	Go to GlyGen: P00734-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin	C [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945 Go to UniProtKB: P09945
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
10U Query on 10U Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	(S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentylamino)ethanoyl)pyrrolidine-2-carboxamide C₂₀ H₂₉ N₅ O₂ WXYKSWZWRHMJTE-KRWDZBQOSA-N		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H]	E [auth H], F [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	C [auth I]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000586 (10U) Query on PRD_000586	G [auth H]	(S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclopentylamino)ethanoyl)pyrrolidine-2-carboxamide	Peptide-like / Thrombin inhibitor		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.263
R-Value Work: 0.164
R-Value Observed: 0.164
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.7	α = 90
b = 71.5	β = 100.9
c = 72.8	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2013-02-27
Changes: Other
Version 1.3: 2016-05-25
Changes: Source and taxonomy
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2023-11-15
Changes: Data collection