MolNFT v1 · #83762 · protein

Reduced hcgd from methanocaldococcus jannaschii

3WSE · Putative GTP cyclohydrolase 1 type 2: “Reduced hcgd from methanocaldococcus jannaschii”. X-ray diffraction, 2 ligands (FE2, PO4), 7 pockets (best druggability 0.77). MolNFT v1 #83762 on GenesisL1: 3D structure, binding sites and…

PDB: 3WSE
Type: protein
Length: 1,473 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative GTP cyclohydrolase 1 type 2
Ligands: FE2, PO4
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative GTP cyclohydrolase 1 type 2	protein	248	39% helix, 23% strand	—
B, C	Putative GTP cyclohydrolase 1 type 2	protein	245	39% helix, 22% strand	—
D	Putative GTP cyclohydrolase 1 type 2	protein	247	39% helix, 23% strand	—
E, F	Putative GTP cyclohydrolase 1 type 2	protein	244	39% helix, 23% strand	—

Ligands and binding sites

FE2 · Fe (II) ion · metal · 12 copies · chains A, B, C, D, E, F
PO4 · Phosphate 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

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.77	0.79	104	FE2, PO4
2	1115	0.76	0.79	103	FE2, PO4
3	749	0.71	0.77	83	FE2, PO4
4	257	0.63	0.81	27	empty
5	363	0.59	0.76	36	empty

Interfaces

6 interfaces between chains.

E–F · 1289 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1283 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1270 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 772 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 742 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3WSE · Reduced 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 3WSE · PDBe 3WSE

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