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Structure of adenosine-5'-phosphosulfate kinase

Analyse Structure of adenosine-5'-phosphosulfate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CB6
Type: protein
Length: 1,038 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable adenylyl-sulfate kinase
EC: 2.7.1.25
UniProt: P72940
Ligands: ADX, ANP, MG, NA
Pockets: 9 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Probable adenylyl-sulfate kinase (EC 2.7.1.25)	protein	173	44% helix, 16% strand	P72940

Ligands and binding sites

ADX · Adenosine-5'-phosphosulfate · ligand · 6 copies · chains A, B, C, D, E, F
ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
NA · Sodium ion · metal · chains A, B
CAC · Cacodylate ion · additive · 2 copies · chains C, F, D, E

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.67	0.82	46	ADX, ANP, NA
2	291	0.66	0.82	46	ADX, ANP
3	240	0.63	0.82	34	ADX, ANP
4	205	0.61	0.82	32	ADX, ANP
5	175	0.61	0.83	32	ADX, ANP

Interfaces

5 interfaces between chains.

A–D · 716 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 695 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 437 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 195 Å² buried · 3 hydrogen bonds · protein-protein
C–F · 190 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5CB6 · Structure of adenosine-5'-phosphosulfate kinase · the same entry in another collection · chain F against F, TM-score 1.00
P72940 · AlphaFold monomer V2.0 prediction for probable adenylyl-sulfate kinase (P72940) · a predicted model of the same protein · chain D 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 P72940
Elsewhere: RCSB PDB 5CB6 · PDBe 5CB6 · UniProt P72940

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