Research workbench
Human PKM2 with L-serine and fbp bound.
Analyse Human PKM2 with L-serine and fbp bound. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B2D
- Type
- protein
- Length
- 2,068 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
- SER, FBP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 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 | 514 | 39% helix, 18% strand | P14618 |
| D | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 518 | 38% helix, 13% strand | P14618 |
Ligands and binding sites
- SER · Serine · 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
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.87 | 0.96 | 55 | empty |
| 2 | 321 | 0.86 | 0.95 | 42 | empty |
| 3 | 1095 | 0.86 | 0.86 | 83 | empty |
| 4 | 953 | 0.78 | 0.80 | 95 | empty |
| 5 | 771 | 0.76 | 0.81 | 86 | MG |
Interfaces
6 interfaces between chains.
- C–D · 2960 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2936 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 1327 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1161 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 1 hydrogen bond · 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 4B2D · PDBe 4B2D · UniProt P14618
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.