MolNFT v1 · #83208 · protein

Hcgb from methanocaldococcus jannaschii

3WB1 · Uncharacterized protein MJ0488: “Hcgb from methanocaldococcus jannaschii”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.87). MolNFT v1 #83208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WB1
Type: protein
Length: 628 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein MJ0488
UniProt: Q57912
Ligands: SO4
Pockets: 7 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Uncharacterized protein MJ0488	protein	157	43% helix, 18% strand	Q57912

Ligands and binding sites

SO4 · Sulfate ion · ion · 19 copies · chains A, D, B, C

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	840	0.87	0.89	50	SO4
2	331	0.64	0.80	35	SO4
3	295	0.62	0.80	33	SO4
4	321	0.62	0.79	35	SO4
5	299	0.61	0.79	28	SO4

Interfaces

6 interfaces between chains.

A–B · 2069 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2061 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 1024 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 998 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 494 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3WB1 · HcgB from Methanocaldococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
Q57912 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ0488 (Q57912) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q57912
Elsewhere: RCSB PDB 3WB1 · PDBe 3WB1 · UniProt Q57912

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