MolNFT v1 · #163427 · protein

Mycobacterial hydrolase 1

6S2Q · Glucosyl-3-phosphoglycerate phosphatase: “Mycobacterial hydrolase 1”. X-ray diffraction, 1 ligand (IOD), 6 pockets (best druggability 0.66). MolNFT v1 #163427 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6S2Q
Type: protein
Length: 842 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucosyl-3-phosphoglycerate phosphatase
EC: 3.1.3.85, 3.1.3.70
UniProt: P9WIC7
Ligands: IOD
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.85, 3.1.3.70)	protein	214	42% helix, 20% strand	P9WIC7
B	Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.85, 3.1.3.70)	protein	210	41% helix, 19% strand	P9WIC7
C	Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.85, 3.1.3.70)	protein	210	42% helix, 18% strand	P9WIC7
D	Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.85, 3.1.3.70)	protein	208	42% helix, 19% strand	P9WIC7

Ligands and binding sites

IOD · Iodide ion · ion · 23 copies · chains A, C, B, D

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

Pockets

6 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	401	0.66	0.80	37	IOD
2	481	0.65	0.77	56	IOD
3	328	0.64	0.80	33	IOD
4	344	0.60	0.78	40	IOD
5	64	0.42	0.81	13	empty

Interfaces

4 interfaces between chains.

C–D · 829 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 811 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 437 Å² buried · 1 hydrogen bond · protein-protein
B–D · 14 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6S2Q · Mycobacterial hydrolase 1 · the same entry in another collection · chain C against C, TM-score 1.00
P9WIC7 · AlphaFold monomer V2.0 prediction for glucosyl-3-phosphoglycerate phosphatase (P9WIC7) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P9WIC7
Elsewhere: RCSB PDB 6S2Q · PDBe 6S2Q · UniProt P9WIC7

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