MolNFT v1 · #157942 · protein
Crystal structure of ribose-phosphate pyrophosphokinase from legionella pneumophila with bound AMP, ADP, and ribose-5-phosphate
6NFE: “Crystal structure of ribose-phosphate pyrophosphokinase from legionella pneumophila with bound AMP, ADP, and…”. X-ray diffraction, 3 ligands (HSX, AMP, ADP), 5 pockets (best druggability 0.47). MolNFT v1 #157942 on GenesisL1: 3D…
- PDB
- 6NFE
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- A0A2S6FBX1
- Ligands
- HSX, AMP, ADP
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 298 | 35% helix, 28% strand | A0A2S6FBX1 |
| B | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 299 | 35% helix, 26% strand | A0A2S6FBX1 |
Ligands and binding sites
- HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- EOH · Ethanol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.47 | 0.82 | 24 | empty |
| 2 | 94 | 0.45 | 0.80 | 22 | empty |
| 3 | 102 | 0.38 | 0.75 | 19 | HSX |
| 4 | 82 | 0.36 | 0.76 | 19 | HSX |
| 5 | 50 | 0.32 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1892 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6NFE · Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila 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 A0A2S6FBX1
- Elsewhere: RCSB PDB 6NFE · PDBe 6NFE · UniProt A0A2S6FBX1
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