MolNFT v1 · #169274 · protein

WOR5 from pyrococcus furiosus, taurine-bound

6X6U · FORMALDEHYDE:FERREDOXIN oxidoreductase WOR5: “WOR5 from pyrococcus furiosus, taurine-bound”. X-ray diffraction, 6 ligands (SF4, PTE, TAU), 15 pockets (best druggability 0.86). MolNFT v1 #169274 on GenesisL1: 3D structure, binding…

PDB: 6X6U
Type: protein
Length: 1,580 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FORMALDEHYDE:FERREDOXIN oxidoreductase WOR5; Oxidoreductase, fe-S subunit
UniProt: I6V2C3, I6U881
Ligands: SF4, PTE, TAU, MG, PO4, CL
Pockets: 15 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	FORMALDEHYDE:FERREDOXIN oxidoreductase WOR5	protein	623	44% helix, 13% strand	I6V2C3
B, D	Oxidoreductase, fe-S subunit	protein	167	38% helix, 13% strand	I6U881

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, B, C, D
PTE · Tungstopterin cofactor · ligand · 2 copies · chains A, C
TAU · 2-aminoethanesulfonic acid · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 4 copies · chains A, C
PO4 · Phosphate ion · ion · 7 copies · chains A, B, D, C
CL · Chloride ion · ion · 3 copies · chains A, B, C, D

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

Pockets

15 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	577	0.86	0.91	52	PO4
2	949	0.80	0.82	85	PTE, SF4, MG, TAU
3	924	0.80	0.82	78	PTE, SF4, MG, TAU
4	50	0.69	0.97	16	empty
5	68	0.55	0.87	13	empty

Interfaces

6 interfaces between chains.

C–D · 2129 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2098 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1140 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1113 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 60 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6X6U · WOR5 from Pyrococcus furiosus, taurine-bound · 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 I6V2C3
Every structure of UniProt I6U881
Elsewhere: RCSB PDB 6X6U · PDBe 6X6U · UniProt I6V2C3 · UniProt I6U881

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