MolNFT v1 · #52067 · protein

Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (pcp)

2VPY · Thiosulfate reductase: “Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (pcp)”. X-ray diffraction, 4 ligands (SF4, MGD, PCI), 20 pockets (best druggability 0.88). MolNFT v1 #52067 on GenesisL1: 3D structure…

PDB: 2VPY
Type: protein
Length: 2,354 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiosulfate reductase; Nrfc protein; Hypothetical membrane spanning protein
UniProt: Q72LA4, Q72LA5, Q72LA6
Ligands: SF4, MGD, PCI, MO
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Thiosulfate reductase	protein	734	29% helix, 16% strand	Q72LA4
B, F	Nrfc protein	protein	193	18% helix, 23% strand	Q72LA5
C, G	Hypothetical membrane spanning protein	protein	250	67% helix, 1% strand	Q72LA6

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, B, E, F
MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · 4 copies · chains A, E
PCI · Pentachlorophenol · ligand · 2 copies · chains B, C, F, G
MO · Molybdenum atom · metal · 2 copies · chains A, E

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1151	0.88	0.90	150	MGD, MO
2	1041	0.88	0.90	130	MGD, MO
3	756	0.83	0.87	93	empty
4	530	0.80	0.86	45	empty
5	407	0.72	0.82	33	empty

Interfaces

9 interfaces between chains.

A–B · 1896 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1819 Å² buried · 20 hydrogen bonds · protein-protein
F–G · 1674 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 1648 Å² buried · 30 hydrogen bonds · protein-protein
C–G · 992 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2VPY · Polysulfide reductase with bound qui inhibitor, pentachlorophenol (PCP) · the same entry in another collection · 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 Q72LA4
Every structure of UniProt Q72LA5
Every structure of UniProt Q72LA6
Elsewhere: RCSB PDB 2VPY · PDBe 2VPY · UniProt Q72LA4 · UniProt Q72LA5 · UniProt Q72LA6

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