MolNFT v1 · #15712 · protein
Crystal structures of human prostatic acid phosphatase in complex with a phosphate ion and alpha-benzylaminobenzylphosphonic acid update the mechanistic picture and offer new insights into inhibitor design
1ND5: “Crystal structures of human prostatic acid phosphatase in complex with a phosphate ion and…”. X-ray diffraction, 4 ligands (2BF, NAG, MAN), 17 pockets (best druggability 0.83). MolNFT v1 #15712 on GenesisL1: 3D structure, binding…
- PDB
- 1ND5
- 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
- 2BF, NAG, MAN, NDG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Prostatic acid phosphatase (EC 3.1.3.2) | protein | 342 | 46% helix, 13% strand | P15309 |
| B | Prostatic acid phosphatase (EC 3.1.3.2) | protein | 342 | 44% helix, 14% strand | P15309 |
Ligands and binding sites
- 2BF · Alpha-benzyl-aminobenzyl-phosphonic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
- 1PE · Pentaethylene glycol · additive · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.83 | 0.84 | 95 | 1PE, 2BF |
| 2 | 437 | 0.74 | 0.84 | 61 | 2BF, 1PE |
| 3 | 447 | 0.66 | 0.78 | 59 | 2BF, 1PE |
| 4 | 293 | 0.62 | 0.79 | 43 | 2BF, 1PE |
| 5 | 192 | 0.58 | 0.81 | 26 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1604 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1591 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 277 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 1ND5 · Crystal Structures of Human Prostatic Acid Phosphatase in Complex with a Phosphate Ion… · the same entry in another collection · chain A against A, TM-score 1.00
- P15309 · AlphaFold monomer V2.0 prediction for prostatic acid phosphatase (P15309) · a predicted model of the same protein · chain B 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 1ND5 · PDBe 1ND5 · UniProt P15309
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