MolNFT v1 · #20695 · protein
Crystal structure of apha class B acid PHOSPHATASE/PHOSPHOTRANSFERASE complexed with adenosine.
1RMT: “Crystal structure of apha class B acid PHOSPHATASE/PHOSPHOTRANSFERASE complexed with adenosine.”. X-ray diffraction, 2 ligands (ADN, MG), 10 pockets (best druggability 0.65). MolNFT v1 #20695 on GenesisL1: 3D structure, binding…
- PDB
- 1RMT
- Type
- protein
- Length
- 838 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class B acid phosphatase
- EC
- 3.1.3.2
- UniProt
- P32697
- Ligands
- ADN, MG
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Class B acid phosphatase (EC 3.1.3.2) | protein | 210 | 37% helix, 16% strand | P32697 |
| C, D | Class B acid phosphatase (EC 3.1.3.2) | protein | 209 | 36% helix, 17% strand | P32697 |
Ligands and binding sites
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.65 | 0.86 | 25 | ADN |
| 2 | 233 | 0.62 | 0.82 | 37 | MG, ADN |
| 3 | 224 | 0.57 | 0.79 | 29 | ADN |
| 4 | 185 | 0.53 | 0.79 | 26 | ADN |
| 5 | 289 | 0.52 | 0.74 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1378 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1367 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 373 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1RMT · Crystal structure of AphA class B acid phosphatase/phosphotransferase complexed with… · 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 P32697
- Elsewhere: RCSB PDB 1RMT · PDBe 1RMT · UniProt P32697
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