MolNFT v1 · #164321 · protein
Trypanosoma congolense pyruvate kinase in complex with citrate and glycerol
6SU1: “Trypanosoma congolense pyruvate kinase in complex with citrate and glycerol”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #164321 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SU1
- Type
- protein
- Length
- 3,765 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- G0UYF4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 439 | 42% helix, 15% strand | G0UYF4 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 476 | 41% helix, 16% strand | G0UYF4 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 499 | 37% helix, 22% strand | G0UYF4 |
| D, F | Pyruvate kinase (EC 2.7.1.40) | protein | 498 | 39% helix, 20% strand | G0UYF4 |
| E | Pyruvate kinase (EC 2.7.1.40) | protein | 495 | 38% helix, 22% strand | G0UYF4 |
| G | Pyruvate kinase (EC 2.7.1.40) | protein | 411 | 45% helix, 15% strand | G0UYF4 |
| H | Pyruvate kinase (EC 2.7.1.40) | protein | 449 | 41% helix, 14% strand | G0UYF4 |
Ligands and binding sites
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F, G, H
- CIT · Citric acid · additive · 6 copies · chains B, C, D, E, F, H
- PGE · Triethylene glycol · additive · chains F
- PEG · Di(hydroxyethyl)ether · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.86 | 0.88 | 124 | empty |
| 2 | 669 | 0.81 | 0.86 | 66 | empty |
| 3 | 505 | 0.81 | 0.88 | 52 | empty |
| 4 | 419 | 0.79 | 0.88 | 38 | empty |
| 5 | 1130 | 0.76 | 0.78 | 107 | CIT |
Interfaces
11 interfaces between chains.
- E–F · 2755 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2708 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2703 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2613 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1126 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6SU1 · 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 6SU1 · PDBe 6SU1 · UniProt G0UYF4
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