MolNFT v1 · #24806 · protein
Crystal structure of phosphoglycerate kinase from thermus thermophilus HB8
1V6S: “Crystal structure of phosphoglycerate kinase from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.59). MolNFT v1 #24806 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1V6S
- Type
- protein
- Length
- 780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- P09403
- Ligands
- NA
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 390 | 40% helix, 17% strand | P09403 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.59 | 0.81 | 34 | empty |
| 2 | 205 | 0.56 | 0.79 | 30 | empty |
| 3 | 111 | 0.40 | 0.75 | 35 | empty |
| 4 | 58 | 0.39 | 0.80 | 23 | empty |
| 5 | 69 | 0.32 | 0.76 | 17 | empty |
Compared structures
- 1V6S · Crystal Structure of Phosphoglycerate Kinase from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- P09403 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (P09403) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P09403
- Elsewhere: RCSB PDB 1V6S · PDBe 1V6S · UniProt P09403
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