2D33

Crystal Structure of gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride

PDB DOI: https://doi.org/10.2210/pdb2D33/pdb

Classification: LIGASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-09-25 Released: 2006-11-14
Deposition Author(s): Hibi, T., Nakayama, M., Nii, H., Kurokawa, Y., Katano, H., Oda, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.191 (Depositor), 0.210 (DCC)
R-Value Work:
0.162 (Depositor), 0.180 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural basis of efficient coupling between peptide ligation and ATP hydrolysis by gamma-gluatamylcysteine synthetase

Hibi, T., Nakayama, M., Nii, H., Kurokawa, Y., Katano, H., Oda, J.

To be published.

Macromolecule Content

Total Structure Weight: 236.51 kDa
Atom Count: 16,327
Modelled Residue Count: 2,016
Deposited Residue Count: 2,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate--cysteine ligase	A, B, C, D	518	Escherichia coli	Mutation(s): 4 Gene Names: gshI EC: 6.3.2.2
UniProt
Find proteins for P0A6W9 (Escherichia coli (strain K12)) Explore P0A6W9 Go to UniProtKB: P0A6W9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6W9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain Y [auth C] MOL2 format, chain R [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain R [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Y [auth C]	FA [auth D], K [auth A], R [auth B], Y [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain FA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Y [auth C]
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	DA [auth D], I [auth A], P [auth B], W [auth C]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C]
CYS Query on CYS Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain EA [auth D] SDF format, chain J [auth A] SDF format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain X [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B]	EA [auth D], J [auth A], Q [auth B], X [auth C]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain EA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Z [auth C]	GA [auth D], L [auth A], S [auth B], Z [auth C]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain GA [auth D] Focus chain L [auth A] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain L [auth A] Focus chain S [auth B] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C]	AA [auth D] BA [auth D] CA [auth D] E [auth A] F [auth A] AA [auth D], BA [auth D], CA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], T [auth C], U [auth C], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]