MolNFT v1 · #72227 · protein
The structure of muscle pyruvate kinase in complex with proline, pyruvate, and MN2+
3N25 · Pyruvate kinase isozymes M1/M2: “The structure of muscle pyruvate kinase in complex with proline, pyruvate, and MN2+”. X-ray diffraction, 5 ligands (PRO, PYR, NA), 20 pockets (best druggability 0.90). MolNFT v1 #72227 on GenesisL1…
- PDB
- 3N25
- Type
- protein
- Length
- 4,125 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
- P11974
- Ligands
- PRO, PYR, NA, MN, K
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 519 | 39% helix, 21% strand | P11974 |
| B | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 508 | 39% helix, 19% strand | P11974 |
| C | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 512 | 39% helix, 20% strand | P11974 |
| D, E | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 521 | 39% helix, 21% strand | P11974 |
| F | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 515 | 39% helix, 20% strand | P11974 |
| G | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 510 | 40% helix, 20% strand | P11974 |
| H | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 519 | 39% helix, 20% strand | P11974 |
Ligands and binding sites
- PRO · Proline · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PYR · Pyruvic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 19 copies · chains A, B, C, D, E, F, H, G
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, C, B, D, E, F, H
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 | 991 | 0.90 | 0.92 | 95 | empty |
| 2 | 395 | 0.87 | 0.95 | 37 | empty |
| 3 | 406 | 0.87 | 0.95 | 39 | empty |
| 4 | 623 | 0.87 | 0.91 | 69 | GOL |
| 5 | 376 | 0.87 | 0.95 | 40 | empty |
Interfaces
15 interfaces between chains.
- E–G · 3042 Ų buried · 40 hydrogen bonds · protein-protein
- F–H · 3033 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 2946 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2908 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1445 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3N25 · The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+ · the same entry in another collection · chain C against C, TM-score 1.00
- P11974 · AlphaFold monomer V2.0 prediction for pyruvate kinase pkm (P11974) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 P11974
- Elsewhere: RCSB PDB 3N25 · PDBe 3N25 · UniProt P11974
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