MolNFT v1 · #121311 · protein
Crystal structure of phosphotriesterase from sphingobium sp. TCM1
5HRM · Haloalkylphosphorus hydrolase: “Crystal structure of phosphotriesterase from sphingobium sp. TCM1”. X-ray diffraction, 1 ligand (MN), 19 pockets (best druggability 0.86). MolNFT v1 #121311 on GenesisL1: 3D structure, binding sites…
- PDB
- 5HRM
- Type
- protein
- Length
- 1,978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkylphosphorus hydrolase
- UniProt
- A0A077JBW9
- Ligands
- MN
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Haloalkylphosphorus hydrolase | protein | 494 | 10% helix, 36% strand | A0A077JBW9 |
| B, D | Haloalkylphosphorus hydrolase | protein | 495 | 9% helix, 36% strand | A0A077JBW9 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.86 | 0.88 | 94 | empty |
| 2 | 1101 | 0.84 | 0.85 | 101 | empty |
| 3 | 150 | 0.81 | 0.96 | 35 | MN |
| 4 | 142 | 0.81 | 0.97 | 35 | empty |
| 5 | 140 | 0.80 | 0.96 | 34 | MN |
Interfaces
5 interfaces between chains.
- C–D · 2271 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2244 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 380 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5HRM · Crystal structure of phosphotriesterase from Sphingobium sp. TCM1 · 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 A0A077JBW9
- Elsewhere: RCSB PDB 5HRM · PDBe 5HRM · UniProt A0A077JBW9
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