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Activator-bound structure of human pyruvate kinase M2
Analyse Activator-bound structure of human pyruvate kinase M2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ME3
- Type
- protein
- Length
- 2,037 residues
- Chains
- 4
- 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
- FBP, 3SZ, UNX, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 518 | 39% helix, 21% strand | P14618 |
| B | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 498 | 40% helix, 19% strand | P14618 |
| C | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 517 | 39% helix, 21% strand | P14618 |
| D | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 504 | 40% helix, 20% strand | P14618 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
- 3SZ · 3-{[4-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)-1,4-diazepan-1-yl]sulfonyl}aniline · ligand · 2 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 42 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.88 | 0.89 | 108 | empty |
| 2 | 430 | 0.87 | 0.95 | 44 | 3SZ |
| 3 | 451 | 0.87 | 0.94 | 53 | 3SZ |
| 4 | 968 | 0.76 | 0.79 | 103 | UNX |
| 5 | 743 | 0.75 | 0.80 | 79 | UNX |
Interfaces
6 interfaces between chains.
- C–D · 2836 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2814 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1329 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1097 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 40 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3ME3 · Activator-Bound Structure of Human Pyruvate Kinase M2 · the same entry in another collection · chain B against B, 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 3ME3 · PDBe 3ME3 · UniProt P14618
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