Research workbench

Crystal structure of pectobacterium carotovorum 2-keto-3-deoxy-D- gluconate dehydrogenase complexed with NAD+

Analyse Crystal structure of pectobacterium carotovorum 2-keto-3-deoxy-D- gluconate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZA2
Type: protein
Length: 980 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-deoxy-D-gluconate 3-dehydrogenase
EC: 1.1.1.127
UniProt: A0A093RP61
Ligands: NAD
Pockets: 9 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-deoxy-D-gluconate 3-dehydrogenase (EC 1.1.1.127)	protein	253	51% helix, 16% strand	A0A093RP61
B	2-deoxy-D-gluconate 3-dehydrogenase (EC 1.1.1.127)	protein	241	49% helix, 17% strand	A0A093RP61
C	2-deoxy-D-gluconate 3-dehydrogenase (EC 1.1.1.127)	protein	239	49% helix, 17% strand	A0A093RP61
D	2-deoxy-D-gluconate 3-dehydrogenase (EC 1.1.1.127)	protein	247	50% helix, 16% strand	A0A093RP61

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · chains D

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

Pockets

9 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	748	0.86	0.89	56	empty
2	1173	0.82	0.83	107	NAD
3	501	0.69	0.79	46	empty
4	496	0.63	0.76	46	empty
5	55	0.46	0.85	12	empty

Interfaces

6 interfaces between chains.

A–B · 1841 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1818 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1516 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1516 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 360 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4ZA2 · Crystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-gluconate dehydrogenase… · 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 A0A093RP61
Elsewhere: RCSB PDB 4ZA2 · PDBe 4ZA2 · UniProt A0A093RP61

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.