MolNFT v1 · #152371 · protein

Crystal structure of the apo form of cmp-N-acetylneuraminate synthetase from vibrio cholerae

6IFI: “Crystal structure of the apo form of cmp-N-acetylneuraminate synthetase from vibrio cholerae”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.57). MolNFT v1 #152371 on GenesisL1: 3D structure, binding sites and…

PDB: 6IFI
Type: protein
Length: 428 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cmp-N-acetylneuraminate synthetase
EC: 2.7.7.43
Ligands: CA
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cmp-N-acetylneuraminate synthetase (EC 2.7.7.43)	protein	210	34% helix, 26% strand	—
B	Cmp-N-acetylneuraminate synthetase (EC 2.7.7.43)	protein	218	33% helix, 25% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.57	0.74	46	empty
2	272	0.52	0.75	33	empty
3	144	0.48	0.77	20	empty

Interfaces

1 interface between chains.

A–B · 1493 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6IFI · Crystal Structure of the Apo form of CMP-N-acetylneuraminate Synthetase from Vibrio… · 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
Elsewhere: RCSB PDB 6IFI · PDBe 6IFI

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