MolNFT v1 · #50126 · protein

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

2R94 · 2-keto-3-deoxy-(6-phospho-)gluconate aldolase: “Crystal structure of KD(P)GA from T.TENAX”. X-ray diffraction, 1 ligand (PYR), 15 pockets (best druggability 0.72). MolNFT v1 #50126 on GenesisL1: 3D structure, binding sites and…

PDB: 2R94
Type: protein
Length: 1,135 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: PYR
Pockets: 15 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-keto-3-deoxy-(6-phospho-)gluconate aldolase (EC 4.1.2.-)	protein	286	51% helix, 14% strand	Q704D1
D	2-keto-3-deoxy-(6-phospho-)gluconate aldolase (EC 4.1.2.-)	protein	281	53% helix, 15% strand	Q704D1
B, C	2-keto-3-deoxy-(6-phospho-)gluconate aldolase (EC 4.1.2.-)	protein	284	53% helix, 14% strand	Q704D1

Ligands and binding sites

PYR · Pyruvic acid · ligand · 4 copies · chains A, D, B, C

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

Pockets

15 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	206	0.72	0.88	26	PYR
2	194	0.72	0.89	27	PYR
3	155	0.69	0.88	28	empty
4	163	0.68	0.88	26	empty
5	184	0.66	0.86	32	empty

Interfaces

4 interfaces between chains.

B–C · 1802 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1788 Å² buried · 19 hydrogen bonds · protein-protein
D–B · 1048 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1013 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).

Compared structures

2R94 · 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 B 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 2R94 · PDBe 2R94 · UniProt Q704D1

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