MolNFT v1 · #52556 · protein

Acylphosphatase variant G91A from pyrococcus horikoshii

2W4D: “Acylphosphatase variant G91A from pyrococcus horikoshii”. X-ray diffraction, 2 ligands (K, PO4), 6 pockets (best druggability 0.70). MolNFT v1 #52556 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2W4D
Type: protein
Length: 540 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acylphosphatase
EC: 3.6.1.7
UniProt: P84142
Ligands: K, PO4
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Acylphosphatase (EC 3.6.1.7)	protein	90	26% helix, 42% strand	P84142

Ligands and binding sites

K · Potassium ion · metal · 6 copies · chains A, E, B, C, D, F
PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.70	0.96	19	empty
2	189	0.48	0.76	24	empty
3	118	0.39	0.75	20	K
4	99	0.35	0.74	16	K
5	73	0.32	0.74	14	empty

Interfaces

9 interfaces between chains.

E–F · 739 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 695 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 692 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 476 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 421 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2W4D · Acylphosphatase variant G91A from Pyrococcus horikoshii · the same entry in another collection · chain F against F, TM-score 1.00
P84142 · AlphaFold monomer V2.0 prediction for acylphosphatase (P84142) · a predicted model of the same protein · chain F 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 P84142
Elsewhere: RCSB PDB 2W4D · PDBe 2W4D · UniProt P84142

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