MolNFT v1 · #114556 · protein
X-ray crystal structure of phosphoglycerate kinase from acinetobacter baumannii
5BT8: “X-ray crystal structure of phosphoglycerate kinase from acinetobacter baumannii”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #114556 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BT8
- Type
- protein
- Length
- 2,376 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- A0A0A2T205
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 396 | 44% helix, 18% strand | A0A0A2T205 |
| B, F | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 397 | 43% helix, 18% strand | A0A0A2T205 |
| D, E | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 395 | 44% helix, 18% strand | A0A0A2T205 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.77 | 0.79 | 108 | empty |
| 2 | 797 | 0.71 | 0.76 | 70 | empty |
| 3 | 510 | 0.65 | 0.77 | 54 | empty |
| 4 | 183 | 0.57 | 0.81 | 41 | empty |
| 5 | 366 | 0.57 | 0.75 | 44 | empty |
Interfaces
7 interfaces between chains.
- A–B · 464 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 434 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 238 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 112 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 101 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5BT8 · X-ray Crystal Structure of phosphoglycerate kinase from Acinetobacter baumannii · 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 A0A0A2T205
- Elsewhere: RCSB PDB 5BT8 · PDBe 5BT8 · UniProt A0A0A2T205
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