MolNFT v1 · #79033 · protein
Human M1 pyruvate kinase
3SRF · Pyruvate kinase isozymes M1/M2: “Human M1 pyruvate kinase”. X-ray diffraction, 4 ligands (PYR, K, MG), 20 pockets (best druggability 0.88). MolNFT v1 #79033 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SRF
- Type
- protein
- Length
- 4,128 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase isozymes M1/M2
- EC
- 2.7.1.40
- UniProt
- P14618
- Ligands
- PYR, K, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 517 | 38% helix, 21% strand | P14618 |
| B | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 517 | 39% helix, 20% strand | P14618 |
| D | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 515 | 39% helix, 21% strand | P14618 |
| E | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 514 | 39% helix, 20% strand | P14618 |
| F | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 516 | 39% helix, 21% strand | P14618 |
| G | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 513 | 38% helix, 20% strand | P14618 |
| H | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 519 | 39% helix, 21% strand | P14618 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 8 copies · chains C, A, B, D, E, F, G, H
- K · Potassium ion · metal · 8 copies · chains C, A, B, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains C, A, B, D, E, F, G, H
- PO4 · Phosphate ion · ion · 8 copies · chains C, A, B, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains C, A, B, D, E, F, G
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 | 818 | 0.88 | 0.91 | 65 | empty |
| 2 | 258 | 0.85 | 0.96 | 36 | empty |
| 3 | 256 | 0.85 | 0.96 | 34 | empty |
| 4 | 270 | 0.85 | 0.96 | 38 | empty |
| 5 | 269 | 0.85 | 0.95 | 36 | empty |
Interfaces
11 interfaces between chains.
- C–D · 3070 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 3019 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 3001 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2999 Ų buried · 35 hydrogen bonds · protein-protein
- C–G · 1493 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3SRF · Human M1 pyruvate kinase · the same entry in another collection · chain C against C, 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 P14618
- Elsewhere: RCSB PDB 3SRF · PDBe 3SRF · UniProt P14618
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