Research workbench
Human M2 pyruvate kinase in complex with fructose 1-6 bisphosphate and oxalate.
Analyse Human M2 pyruvate kinase in complex with fructose 1-6 bisphosphate and oxalate. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SRD
- Type
- protein
- Length
- 2,056 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
- OXL, FBP, MG, K
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 515 | 39% helix, 21% strand | P14618 |
| B | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 512 | 39% helix, 21% strand | P14618 |
| C | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 514 | 39% helix, 21% strand | P14618 |
| D | Pyruvate kinase isozymes M1/M2 (EC 2.7.1.40) | protein | 515 | 39% helix, 21% strand | P14618 |
Ligands and binding sites
- OXL · Oxalate ion · 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 · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 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 | 1157 | 0.87 | 0.88 | 103 | empty |
| 2 | 385 | 0.86 | 0.95 | 62 | empty |
| 3 | 336 | 0.86 | 0.95 | 42 | empty |
| 4 | 1090 | 0.83 | 0.84 | 132 | OXL, MG, K, GOL |
| 5 | 583 | 0.78 | 0.84 | 73 | OXL, K, MG |
Interfaces
6 interfaces between chains.
- A–C · 3081 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 3078 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1349 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1349 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SRD · Human M2 pyruvate kinase in complex with fructose 1-6 bisphosphate and Oxalate. · the same entry in another collection · chain A against A, 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 3SRD · PDBe 3SRD · UniProt P14618
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