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Structure of M2 pyruvate kinase in complex with phenylalanine
Analyse Structure of M2 pyruvate kinase in complex with phenylalanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FXJ
- Type
- protein
- Length
- 1,923 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
- PHE, PO4
- Pockets
- 20 · best druggability 0.85
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 | 498 | 38% helix, 21% strand | P14618 |
| B | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 413 | 45% helix, 15% strand | P14618 |
| C | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 504 | 39% helix, 21% strand | P14618 |
| D | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 508 | 38% helix, 21% strand | P14618 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 5 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.85 | 0.95 | 41 | empty |
| 2 | 728 | 0.82 | 0.86 | 70 | empty |
| 3 | 1005 | 0.78 | 0.80 | 94 | PO4 |
| 4 | 983 | 0.77 | 0.80 | 93 | empty |
| 5 | 746 | 0.72 | 0.78 | 69 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2630 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2548 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1231 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1119 Ų buried · 18 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 4FXJ · PDBe 4FXJ · UniProt P14618
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