MolNFT v1 · #25148 · protein

Crystal structure of cmp-kdo synthetase

1VH1 · 3-deoxy-manno-octulosonate cytidylyltransferase: “Crystal structure of cmp-kdo synthetase”. X-ray diffraction, 14 pockets (best druggability 0.74). MolNFT v1 #25148 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VH1
Type: protein
Length: 937 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-deoxy-manno-octulosonate cytidylyltransferase
EC: 2.7.7.38
UniProt: P04951
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38)	protein	239	34% helix, 23% strand	P04951
B	3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38)	protein	224	34% helix, 24% strand	P04951
C	3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38)	protein	233	36% helix, 24% strand	P04951
D	3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38)	protein	241	34% helix, 23% strand	P04951

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	826	0.74	0.79	81	empty
2	92	0.67	0.92	18	empty
3	565	0.63	0.75	53	empty
4	396	0.59	0.76	51	empty
5	82	0.56	0.86	20	empty

Interfaces

5 interfaces between chains.

A–B · 1194 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1194 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 527 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 447 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 429 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

1VH1 · Crystal structure of CMP-KDO synthetase · the same entry in another collection · chain D against D, TM-score 1.00
P04951 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain D against A, TM-score 0.97

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 P04951
Elsewhere: RCSB PDB 1VH1 · PDBe 1VH1 · UniProt P04951

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