MolNFT v1 · #83761 · protein

Oxidized hcgd from methanocaldococcus jannaschii

3WSD · Putative GTP cyclohydrolase 1 type 2: “Oxidized hcgd from methanocaldococcus jannaschii”. X-ray diffraction, 2 ligands (FE, CL), 8 pockets (best druggability 0.76). MolNFT v1 #83761 on GenesisL1: 3D structure, binding sites and…

PDB: 3WSD
Type: protein
Length: 1,470 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative GTP cyclohydrolase 1 type 2
Ligands: FE, CL
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Putative GTP cyclohydrolase 1 type 2	protein	247	39% helix, 23% strand	—
B, C, E, F	Putative GTP cyclohydrolase 1 type 2	protein	244	39% helix, 22% strand	—

Ligands and binding sites

FE · Fe (III) ion · metal · 12 copies · chains A, F, B, D, C, E
CL · Chloride ion · ion · 6 copies · chains A, F, B, D, C, E

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

Pockets

8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1075	0.76	0.78	100	FE, CL
2	676	0.73	0.79	84	FE, CL
3	748	0.72	0.78	78	FE, CL
4	269	0.68	0.83	26	empty
5	278	0.66	0.82	27	empty

Interfaces

6 interfaces between chains.

A–B · 1271 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1232 Å² buried · 31 hydrogen bonds · protein-protein
E–F · 1218 Å² buried · 31 hydrogen bonds · protein-protein
C–E · 832 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 774 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3WSD · Oxidized HcgD from Methanocaldococcus jannaschii · 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
Elsewhere: RCSB PDB 3WSD · PDBe 3WSD

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