MolNFT v1 · #93904 · protein

Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero-D- galactonononate-9-phosphate phosphohydrolase from bacteroides thetaiotaomicron

4HGR · Acylneuraminate cytidylyltransferase: “Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero-D- galactonononate-9-phosphate…”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.84). MolNFT v1 #93904 on…

PDB: 4HGR
Type: protein
Length: 1,302 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acylneuraminate cytidylyltransferase
UniProt: Q8A712
Ligands: MG
Pockets: 15 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Acylneuraminate cytidylyltransferase	protein	163	39% helix, 19% strand	Q8A712
B, D	Acylneuraminate cytidylyltransferase	protein	163	39% helix, 17% strand	Q8A712
C	Acylneuraminate cytidylyltransferase	protein	162	39% helix, 18% strand	Q8A712
E	Acylneuraminate cytidylyltransferase	protein	164	37% helix, 17% strand	Q8A712
F, H	Acylneuraminate cytidylyltransferase	protein	162	39% helix, 17% strand	Q8A712

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	576	0.84	0.89	106	empty
2	443	0.83	0.90	65	empty
3	523	0.82	0.88	67	empty
4	370	0.59	0.76	39	MG
5	338	0.57	0.76	37	MG

Interfaces

20 interfaces between chains.

B–D · 1276 Å² buried · 17 hydrogen bonds · protein-protein
F–H · 1258 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1212 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1200 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1169 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4HGR · Crystal structure of E56A/K67A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phos… · the same entry in another collection · chain H against H, TM-score 1.00
Q8A712 · AlphaFold monomer V2.0 prediction for 2-keto-3-deoxy-D-glycero-D… · a predicted model of the same protein · 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 Q8A712
Elsewhere: RCSB PDB 4HGR · PDBe 4HGR · UniProt Q8A712

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