MolNFT v1 · #26042 · protein

Crystal structure of uroporphyrinogen III synthase from an extremely thermophilic bacterium thermus thermophilus HB8 (wild type, native, form-2 crystal)

1WD7: “Crystal structure of uroporphyrinogen III synthase from an extremely thermophilic bacterium thermus…”. X-ray diffraction, 4 pockets (best druggability 0.71). MolNFT v1 #26042 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1WD7
Type: protein
Length: 509 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uroporphyrinogen III synthase
EC: 4.2.1.75
UniProt: Q5SKH2
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uroporphyrinogen III synthase (EC 4.2.1.75)	protein	254	46% helix, 19% strand	Q5SKH2
B	Uroporphyrinogen III synthase (EC 4.2.1.75)	protein	255	45% helix, 19% strand	Q5SKH2

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	722	0.71	0.78	62	empty
2	326	0.60	0.77	38	empty
3	85	0.42	0.79	15	empty
4	64	0.36	0.78	15	empty

Interfaces

1 interface between chains.

A–B · 640 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1WD7 · Crystal Structure of Uroporphyrinogen III Synthase from an Extremely Thermophilic… · 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 Q5SKH2
Elsewhere: RCSB PDB 1WD7 · PDBe 1WD7 · UniProt Q5SKH2

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