MolNFT v1 · #167052 · protein

Agrobacterium tumefaciens ADP-glucose pyrophosphorylase-S72D

6V9A · Glucose-1-phosphate adenylyltransferase: “Agrobacterium tumefaciens ADP-glucose pyrophosphorylase-S72D”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #167052 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6V9A
Type: protein
Length: 8,290 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose-1-phosphate adenylyltransferase
EC: 2.7.7.27
UniProt: Q8U8L5
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A, B, D, E, F, G, I, K, L, M, N, O, P, Q, R, V, T	Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)	protein	415	28% helix, 29% strand	Q8U8L5
C	Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)	protein	412	28% helix, 29% strand	Q8U8L5
J	Glucose-1-phosphate adenylyltransferase (EC 2.7.7.27)	protein	408	29% helix, 30% strand	Q8U8L5

Ligands and binding sites

GOL · Glycerol · additive · 22 copies · chains H, G, A, B, C, D, E, F, I, J, K, L, M, N, O, P, Q, R, V, T
CIT · Citric acid · additive · 20 copies · chains H, G, A, B, C, D, E, F, I, J, K, L, M, N, O, P, Q, R, V, T

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	905	0.88	0.90	92	empty
2	892	0.87	0.90	84	empty
3	805	0.87	0.90	76	empty
4	805	0.84	0.87	84	empty
5	883	0.84	0.86	84	empty

Interfaces

34 interfaces between chains.

A–B · 1464 Å² buried · 18 hydrogen bonds · protein-protein
M–N · 1456 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1453 Å² buried · 20 hydrogen bonds · protein-protein
O–P · 1442 Å² buried · 21 hydrogen bonds · protein-protein
H–G · 1440 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6V9A · Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase-S72D · the same entry in another collection · chain K against K, 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 Q8U8L5
Elsewhere: RCSB PDB 6V9A · PDBe 6V9A · UniProt Q8U8L5

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