MolNFT v1 · #61063 · protein
2.3 a crystal structure of ribose-phosphate pyrophosphokinase from burkholderia pseudomallei
3DAH: “2.3 a crystal structure of ribose-phosphate pyrophosphokinase from burkholderia pseudomallei”. X-ray diffraction, 2 ligands (AMP, PO4), 6 pockets (best druggability 0.74). MolNFT v1 #61063 on GenesisL1: 3D structure, binding sites…
- PDB
- 3DAH
- Type
- protein
- Length
- 884 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- Q3JW86
- Ligands
- AMP, PO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 290 | 35% helix, 24% strand | Q3JW86 |
| B | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 294 | 37% helix, 24% strand | Q3JW86 |
| C | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 300 | 36% helix, 26% strand | Q3JW86 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.74 | 0.77 | 90 | PO4 |
| 2 | 270 | 0.58 | 0.78 | 31 | PO4 |
| 3 | 87 | 0.53 | 0.85 | 16 | PO4 |
| 4 | 181 | 0.44 | 0.74 | 25 | empty |
| 5 | 62 | 0.35 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1945 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1318 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3DAH · 2.3 A crystal structure of ribose-phosphate pyrophosphokinase from Burkholderia… · 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 Q3JW86
- Elsewhere: RCSB PDB 3DAH · PDBe 3DAH · UniProt Q3JW86
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