Research workbench
Complex structure of pctv K276R mutant with pmp and 3-dehydroshkimate
Analyse Complex structure of pctv K276R mutant with pmp and 3-dehydroshkimate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZM4
- Type
- protein
- Length
- 2,490 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- UniProt
- A8R0K5
- Ligands
- PLP, P3B
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Aminotransferase | protein | 418 | 40% helix, 18% strand | A8R0K5 |
| B, E | Aminotransferase | protein | 425 | 39% helix, 17% strand | A8R0K5 |
| C | Aminotransferase | protein | 417 | 40% helix, 18% strand | A8R0K5 |
| D | Aminotransferase | protein | 387 | 37% helix, 16% strand | A8R0K5 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D, E, F
- P3B · (3E,4R,5R)-4,5-dihydroxy-3-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}cyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.75 | 0.98 | 26 | empty |
| 2 | 76 | 0.75 | 0.98 | 23 | empty |
| 3 | 378 | 0.74 | 0.85 | 56 | PLP |
| 4 | 76 | 0.74 | 0.98 | 24 | empty |
| 5 | 353 | 0.72 | 0.84 | 65 | PLP |
Interfaces
7 interfaces between chains.
- C–D · 4673 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 4672 Ų buried · 84 hydrogen bonds · protein-protein
- E–F · 4658 Ų buried · 81 hydrogen bonds · protein-protein
- C–F · 207 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 176 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ZM4 · Complex structure of PctV K276R mutant with PMP and 3-dehydroshkimate · 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 A8R0K5
- Elsewhere: RCSB PDB 4ZM4 · PDBe 4ZM4 · UniProt A8R0K5
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