MolNFT v1 · #40640 · protein

PRODUCT RUP

2IYP · 6-phosphogluconate dehydrogenase, decarboxylating: “PRODUCT RUP”. X-ray diffraction, 3 ligands (A2P, NAP, 5RP), 12 pockets (best druggability 0.73). MolNFT v1 #40640 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2IYP
Type: protein
Length: 1,407 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-phosphogluconate dehydrogenase, decarboxylating
EC: 1.1.1.44
UniProt: P96789
Ligands: A2P, NAP, 5RP
Pockets: 12 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	protein	469	56% helix, 10% strand	P96789
B	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	protein	470	56% helix, 10% strand	P96789
C	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	protein	468	56% helix, 9% strand	P96789

Ligands and binding sites

A2P · Adenosine-2'-5'-diphosphate · ligand · 2 copies · chains B, C
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, B
5RP · Ribulose-5-phosphate · ligand · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.73	0.98	27	empty
2	372	0.68	0.81	45	NAP, 5RP
3	434	0.63	0.77	45	empty
4	492	0.63	0.76	29	empty
5	336	0.54	0.74	46	A2P

Interfaces

2 interfaces between chains.

A–B · 6150 Å² buried · 67 hydrogen bonds · protein-protein
A–C · 498 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2IYP · product rup · the same entry in another collection · chain A against A, TM-score 1.00
P96789 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, decarboxylating… · a predicted model of the same protein · chain C 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 P96789
Elsewhere: RCSB PDB 2IYP · PDBe 2IYP · UniProt P96789

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