MolNFT v1 · #108323 · protein

Crystal structure of cyma from klebsiella oxytoca

4V3G · Cyma protein: “Crystal structure of cyma from klebsiella oxytoca”. X-ray diffraction, 11 pockets (best druggability 0.81). MolNFT v1 #108323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4V3G
Type: protein
Length: 652 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyma protein
UniProt: Q48391
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 73% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyma protein	protein	330	6% helix, 72% strand	Q48391
B	Cyma protein	protein	322	5% helix, 74% strand	Q48391

Ligands and binding sites

C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 10 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	960	0.81	0.83	100	empty
2	895	0.80	0.82	90	empty
3	465	0.71	0.80	46	C8E
4	183	0.62	0.84	33	C8E
5	71	0.55	0.87	13	empty

Interfaces

1 interface between chains.

A–B · 946 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

4V3G · Crystal structure of CymA from Klebsiella oxytoca · the same entry in another collection · chain A against A, 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 Q48391
Elsewhere: RCSB PDB 4V3G · PDBe 4V3G · UniProt Q48391

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