MolNFT v1 · #158445 · protein
Crystal structure of human PKM2 in complex with L-cysteine
6NU1 · Pyruvate kinase pkm: “Crystal structure of human PKM2 in complex with L-cysteine”. X-ray diffraction, 5 ligands (CYS, FBP, OXL), 20 pockets (best druggability 0.74). MolNFT v1 #158445 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NU1
- Type
- protein
- Length
- 1,959 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase pkm
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- CYS, FBP, OXL, MG, K
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 476 | 41% helix, 17% strand | P14618 |
| B | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 452 | 43% helix, 16% strand | P14618 |
| C | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 516 | 39% helix, 21% strand | P14618 |
| D | Pyruvate kinase pkm (EC 2.7.1.40) | protein | 515 | 39% helix, 21% strand | P14618 |
Ligands and binding sites
- CYS · Cysteine · ligand · 4 copies · chains A, B, C, D
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- OXL · Oxalate ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 2 copies · chains B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.74 | 0.81 | 63 | MG, OXL |
| 2 | 822 | 0.73 | 0.78 | 85 | MG, OXL |
| 3 | 528 | 0.72 | 0.81 | 54 | MG, OXL, K |
| 4 | 522 | 0.68 | 0.78 | 68 | MG, OXL, K |
| 5 | 53 | 0.67 | 0.96 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–D · 357 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 233 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 232 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 136 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P14618
- Elsewhere: RCSB PDB 6NU1 · PDBe 6NU1 · UniProt P14618
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