2D32 | pdb_00002d32

Crystal Structure of Michaelis Complex of gamma-Glutamylcysteine Synthetase

PDB DOI: https://doi.org/10.2210/pdb2D32/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: 2.40 Å
R-Value Free:
0.198 (Depositor), 0.208 (DCC)
R-Value Work:
0.168 (Depositor), 0.179 (DCC)
R-Value Observed:
0.170 (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 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: 236.49 kDa
Atom Count: 16,833
Modeled Residue Count: 2,012
Deposited Residue Count: 2,072
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6W9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth D]	CA [auth D], K [auth A], Q [auth B], W [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain CA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Focus chain W [auth C]
GLU Query on GLU Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain AA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth D]	AA [auth D], I [auth A], O [auth B], U [auth C]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C]
CYS Query on CYS Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth D]	BA [auth D], J [auth A], P [auth B], V [auth C]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] L [auth B] E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], X [auth D], Y [auth D], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]