MolNFT v1 · #50123 · protein

Crystal structure of KD(P)GA from T.TENAX

2R91 · 2-keto-3-deoxy-(6-phospho-)gluconate aldolase: “Crystal structure of KD(P)GA from T.TENAX”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.71). MolNFT v1 #50123 on GenesisL1: 3D structure, binding sites and…

PDB: 2R91
Type: protein
Length: 1,144 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-keto-3-deoxy-(6-phospho-)gluconate aldolase
EC: 4.1.2.-
UniProt: Q704D1
Ligands: SO4
Pockets: 13 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, B, C	2-keto-3-deoxy-(6-phospho-)gluconate aldolase (EC 4.1.2.-)	protein	286	53% helix, 14% strand	Q704D1

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, C

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	147	0.71	0.90	27	SO4
2	295	0.70	0.84	40	SO4
3	154	0.69	0.88	26	SO4
4	135	0.68	0.89	24	SO4
5	208	0.68	0.86	34	empty

Interfaces

4 interfaces between chains.

B–C · 1849 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1822 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1046 Å² buried · 14 hydrogen bonds · protein-protein
D–B · 997 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2R91 · Crystal Structure of KD(P)GA from T.tenax · the same entry in another collection · chain A against A, TM-score 1.00
Q704D1 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxy-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 Q704D1
Elsewhere: RCSB PDB 2R91 · PDBe 2R91 · UniProt Q704D1

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