MolNFT v1 · #46488 · protein
Structure of the E. COLI dihydroneopterin triphosphate pyrophosphohydrolase in complex with SM+3 and pyrophosphate
2O5W · Datp pyrophosphohydrolase: “Structure of the E. COLI dihydroneopterin triphosphate pyrophosphohydrolase in complex with SM+3 and…”. X-ray diffraction, 4 ligands (PPV, SM, NA), 6 pockets (best druggability 0.74). MolNFT v1 #46488 on…
- PDB
- 2O5W
- Type
- protein
- Length
- 577 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Datp pyrophosphohydrolase
- EC
- 3.6.1.-
- UniProt
- P0AFC0
- Ligands
- PPV, SM, NA, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Datp pyrophosphohydrolase (EC 3.6.1.-) | protein | 147 | 26% helix, 33% strand | P0AFC0 |
| B | Datp pyrophosphohydrolase (EC 3.6.1.-) | protein | 147 | 24% helix, 37% strand | P0AFC0 |
| C | Datp pyrophosphohydrolase (EC 3.6.1.-) | protein | 142 | 28% helix, 34% strand | P0AFC0 |
| D | Datp pyrophosphohydrolase (EC 3.6.1.-) | protein | 141 | 21% helix, 30% strand | P0AFC0 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains A, C
- SM · Samarium (III) ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.74 | 0.77 | 94 | empty |
| 2 | 304 | 0.69 | 0.84 | 37 | SO4, SM |
| 3 | 272 | 0.68 | 0.84 | 34 | SO4, SM, NA, PPV |
| 4 | 204 | 0.67 | 0.85 | 32 | SM, NA, PPV |
| 5 | 323 | 0.61 | 0.78 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 449 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 268 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 233 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 209 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 87 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2O5W · Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P0AFC0 · AlphaFold monomer V2.0 prediction for dihydroneopterin triphosphate diphosphatase (P0AFC0) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P0AFC0
- Elsewhere: RCSB PDB 2O5W · PDBe 2O5W · UniProt P0AFC0
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