MolNFT v1 · #164322 · protein
Trypanosoma congolense pyruvate kinase in complex with citrate and glycerol
6SU2: “Trypanosoma congolense pyruvate kinase in complex with citrate and glycerol”. X-ray diffraction, 2 ligands (FBP, MG), 20 pockets (best druggability 0.78). MolNFT v1 #164322 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6SU2
- Type
- protein
- Length
- 1,974 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- G0UYF4
- Ligands
- FBP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Pyruvate kinase (EC 2.7.1.40) | protein | 498 | 39% helix, 21% strand | G0UYF4 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 481 | 40% helix, 20% strand | G0UYF4 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 497 | 38% helix, 20% strand | G0UYF4 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.78 | 0.81 | 91 | empty |
| 2 | 148 | 0.76 | 0.93 | 43 | empty |
| 3 | 940 | 0.75 | 0.78 | 85 | empty |
| 4 | 390 | 0.66 | 0.80 | 46 | MG |
| 5 | 577 | 0.66 | 0.76 | 71 | FBP |
Interfaces
4 interfaces between chains.
- A–D · 1143 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1006 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 199 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6SU2 · Trypanosoma congolense pyruvate kinase in complex with citrate and glycerol · 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 G0UYF4
- Elsewhere: RCSB PDB 6SU2 · PDBe 6SU2 · UniProt G0UYF4
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