MolNFT v1 · #108324 · protein

Crystal structure of cyma from klebsiella oxytoca

4V3H · Cyma protein: “Crystal structure of cyma from klebsiella oxytoca”. X-ray diffraction, 1 ligand (NO3), 8 pockets (best druggability 0.72). MolNFT v1 #108324 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4V3H
Type: protein
Length: 621 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyma protein
UniProt: Q48391
Ligands: NO3
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 77% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyma protein	protein	314	2% helix, 76% strand	Q48391
B	Cyma protein	protein	307	1% helix, 78% strand	Q48391

Ligands and binding sites

NO3 · Nitrate ion · ion · chains B
C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 14 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	720	0.72	0.78	57	C8E
2	481	0.62	0.76	59	empty
3	249	0.51	0.75	37	empty
4	196	0.50	0.77	28	empty
5	120	0.42	0.76	21	C8E

Interfaces

1 interface between chains.

A–B · 691 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4V3H · 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 4V3H · PDBe 4V3H · UniProt Q48391

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