Research workbench
Crystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772
Analyse Crystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ED7
- Type
- protein
- Length
- 3,432 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-diamino-pelargonic acid aminotransferase
- EC
- 2.6.1.62
- UniProt
- A0A0A0GYM0
- Ligands
- J4J, PLP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 7,8-diamino-pelargonic acid aminotransferase (EC 2.6.1.62) | protein | 429 | 39% helix, 20% strand | A0A0A0GYM0 |
Ligands and binding sites
- J4J · 2-[(2-nitrophenyl)sulfanyl]acetohydrazide · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.84 | 0.87 | 124 | PLP, J4J |
| 2 | 640 | 0.83 | 0.87 | 89 | PLP, J4J |
| 3 | 483 | 0.82 | 0.89 | 69 | PLP, J4J |
| 4 | 509 | 0.81 | 0.88 | 71 | PLP, J4J |
| 5 | 815 | 0.80 | 0.83 | 96 | PLP, J4J |
Interfaces
16 interfaces between chains.
- C–D · 5066 Ų buried · 75 hydrogen bonds · protein-protein
- A–B · 5061 Ų buried · 71 hydrogen bonds · protein-protein
- G–H · 5029 Ų buried · 76 hydrogen bonds · protein-protein
- E–F · 4965 Ų buried · 77 hydrogen bonds · protein-protein
- B–D · 473 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6ED7 · Crystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772 · 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 A0A0A0GYM0
- Elsewhere: RCSB PDB 6ED7 · PDBe 6ED7 · UniProt A0A0A0GYM0
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