MolNFT v1 · #127875 · protein

Crystal structure of gatd - a glutamine amidotransferase from staphylococcus aureus involved in peptidoglycan amidation

5N9M · Cobyric acid synthase: “Crystal structure of gatd - a glutamine amidotransferase from staphylococcus aureus involved in peptidoglycan…”. X-ray diffraction, 1 ligand (GLN), 2 pockets (best druggability 0.77). MolNFT v1 #127875 on…

PDB: 5N9M
Type: protein
Length: 482 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cobyric acid synthase
UniProt: A0A0H2WZ38
Ligands: GLN
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cobyric acid synthase	protein	243	30% helix, 32% strand	A0A0H2WZ38
B	Cobyric acid synthase	protein	239	30% helix, 33% strand	A0A0H2WZ38

Ligands and binding sites

GLN · Glutamine · ligand · chains A
PG4 · Tetraethylene glycol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	819	0.77	0.81	93	empty
2	100	0.49	0.81	23	empty

Interfaces

1 interface between chains.

A–B · 632 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5N9M · Crystal structure of GatD - a glutamine amidotransferase from Staphylococcus aureus… · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A0H2WZ38
Elsewhere: RCSB PDB 5N9M · PDBe 5N9M · UniProt A0A0H2WZ38

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