MolNFT v1 · #3540 · protein

Crystal structure of human prostatic acid phosphatase

1CVI: “Crystal structure of human prostatic acid phosphatase”. X-ray diffraction, 5 ligands (GLY, NAG, BMA), 17 pockets (best druggability 0.78). MolNFT v1 #3540 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1CVI
Type: protein
Length: 1,368 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Prostatic acid phosphatase
EC: 3.1.3.2
UniProt: P15309
Ligands: GLY, NAG, BMA, MAN, FUC
Pockets: 17 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Prostatic acid phosphatase (EC 3.1.3.2)	protein	342	46% helix, 15% strand	P15309

Ligands and binding sites

GLY · Glycine · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 9 copies · chains B, D
MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, D
FUC · alpha-L-fucopyranose · sugar

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

Pockets

17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	701	0.78	0.83	74	GLY
2	351	0.68	0.81	33	empty
3	344	0.68	0.82	38	GLY
4	442	0.66	0.79	51	empty
5	325	0.63	0.79	44	GLY

Interfaces

5 interfaces between chains.

A–B · 1504 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1480 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 482 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 405 Å² buried · 1 hydrogen bond · protein-protein
B–D · 328 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan, 8 disulfide (N-glycosylation, disulfide).

Compared structures

1CVI · Crystal structure of human prostatic acid phosphatase · the same entry in another collection · chain D against D, TM-score 1.00
P15309 · AlphaFold monomer V2.0 prediction for prostatic acid phosphatase (P15309) · a predicted model of the same protein · chain D 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 P15309
Elsewhere: RCSB PDB 1CVI · PDBe 1CVI · UniProt P15309

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