MolNFT v1 · #25564 · protein

Chromosome segregation protein SPO0J from thermus thermophilus

1VZ0 · Chromosome-partitioning protein SPO0J: “Chromosome segregation protein SPO0J from thermus thermophilus”. X-ray diffraction, 2 ligands (CO, MG), 13 pockets (best druggability 0.77). MolNFT v1 #25564 on GenesisL1: 3D structure…

PDB: 1VZ0
Type: protein
Length: 1,511 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromosome-partitioning protein SPO0J
UniProt: Q72H91
Ligands: CO, MG
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 60% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Chromosome-partitioning protein SPO0J	protein	186	61% helix, 13% strand	Q72H91
B, D	Chromosome-partitioning protein SPO0J	protein	192	60% helix, 12% strand	Q72H91
C	Chromosome-partitioning protein SPO0J	protein	189	61% helix, 13% strand	Q72H91
E	Chromosome-partitioning protein SPO0J	protein	191	59% helix, 13% strand	Q72H91
F	Chromosome-partitioning protein SPO0J	protein	188	58% helix, 13% strand	Q72H91
H	Chromosome-partitioning protein SPO0J	protein	187	60% helix, 12% strand	Q72H91

Ligands and binding sites

CO · Cobalt (II) ion · metal · 13 copies · chains A, C, B, G, E, D, H, F
MG · Magnesium ion · metal · 2 copies · chains C, D

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

Pockets

13 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	890	0.77	0.80	71	CO
2	872	0.76	0.80	65	empty
3	899	0.76	0.79	68	empty
4	852	0.75	0.79	66	empty
5	998	0.74	0.77	81	CO

Interfaces

13 interfaces between chains.

E–F · 3979 Å² buried · 77 hydrogen bonds · protein-protein
D–H · 3966 Å² buried · 72 hydrogen bonds · protein-protein
B–G · 3956 Å² buried · 79 hydrogen bonds · protein-protein
A–C · 3849 Å² buried · 79 hydrogen bonds · protein-protein
A–H · 386 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1VZ0 · Chromosome segregation protein Spo0J from Thermus thermophilus · the same entry in another collection · chain H against H, TM-score 1.00
Q72H91 · AlphaFold monomer V2.0 prediction for chromosome-partitioning protein SPO0J (Q72H91) · a predicted model of the same protein · chain E against A, TM-score 0.89

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 Q72H91
Elsewhere: RCSB PDB 1VZ0 · PDBe 1VZ0 · UniProt Q72H91

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