MolNFT v1 · #47518 · protein
Crystal structure of a putative phosphonopyruvate hydrolase (MLL9387) from mesorhizobium loti MAFF303099 at 2.15 a resolution
2P10 · MLL9387 protein: “Crystal structure of a putative phosphonopyruvate hydrolase (MLL9387) from mesorhizobium loti MAFF303099 at…”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.77). MolNFT v1 #47518 on GenesisL1…
- PDB
- 2P10
- Type
- protein
- Length
- 1,609 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MLL9387 protein
- UniProt
- Q981G2
- Ligands
- CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MLL9387 protein | protein | 268 | 53% helix, 15% strand | Q981G2 |
| B | MLL9387 protein | protein | 268 | 53% helix, 15% strand | Q981G2 |
| C | MLL9387 protein | protein | 270 | 52% helix, 16% strand | Q981G2 |
| D | MLL9387 protein | protein | 268 | 53% helix, 16% strand | Q981G2 |
| E | MLL9387 protein | protein | 269 | 53% helix, 16% strand | Q981G2 |
| F | MLL9387 protein | protein | 266 | 53% helix, 15% strand | Q981G2 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, F, D
- ACT · Acetate ion · additive · 13 copies · chains A, E, B, D, C, F
- GOL · Glycerol · additive · 4 copies · chains A, F, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.77 | 0.82 | 97 | ACT |
| 2 | 62 | 0.68 | 0.95 | 18 | ACT |
| 3 | 77 | 0.67 | 0.93 | 19 | CL |
| 4 | 199 | 0.65 | 0.84 | 29 | empty |
| 5 | 240 | 0.60 | 0.80 | 51 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2573 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2482 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2434 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1462 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1446 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 2P10 · Crystal structure of a putative phosphonopyruvate hydrolase (MLL9387) from mesorhizobium… · the same entry in another collection · chain F against F, 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 Q981G2
- Elsewhere: RCSB PDB 2P10 · PDBe 2P10 · UniProt Q981G2
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