MolNFT v1 · #56716 · protein

Crystal structure of selenophosphate synthetase from aquifex aeolicus

2ZOD · Selenide, water dikinase: “Crystal structure of selenophosphate synthetase from aquifex aeolicus”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.83). MolNFT v1 #56716 on GenesisL1: 3D structure, binding sites and…

PDB: 2ZOD
Type: protein
Length: 636 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Selenide, water dikinase
EC: 2.7.9.3
UniProt: O67139
Ligands: SO4
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Selenide, water dikinase (EC 2.7.9.3)	protein	315	42% helix, 23% strand	O67139
B	Selenide, water dikinase (EC 2.7.9.3)	protein	321	40% helix, 24% strand	O67139

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

5 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	1127	0.83	0.84	79	SO4
2	1182	0.82	0.83	83	SO4
3	55	0.34	0.78	16	empty
4	71	0.32	0.75	16	empty
5	52	0.31	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 2368 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2ZOD · Crystal structure of selenophosphate synthetase from Aquifex aeolicus · 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 O67139
Elsewhere: RCSB PDB 2ZOD · PDBe 2ZOD · UniProt O67139

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