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Crystal structure of 7,8-diaminopelargonic acid synthase in complex with the cis isomer of amiclenomycin
Analyse Crystal structure of 7,8-diaminopelargonic acid synthase in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MLY
- Type
- protein
- Length
- 855 residues
- Chains
- 2
- 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
- P12995
- Ligands
- ACZ, PLP, NA
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-diamino-pelargonic acid aminotransferase (EC 2.6.1.62) | protein | 427 | 41% helix, 19% strand | P12995 |
| B | 7,8-diamino-pelargonic acid aminotransferase (EC 2.6.1.62) | protein | 428 | 39% helix, 20% strand | P12995 |
Ligands and binding sites
- ACZ · Cis-amiclenomycin · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.80 | 0.84 | 85 | ACZ, PLP |
| 2 | 646 | 0.78 | 0.83 | 84 | ACZ, PLP |
| 3 | 51 | 0.26 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 5213 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 1MLY · Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer… · the same entry in another collection · chain A against A, TM-score 1.00
- P12995 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · a predicted model of the same protein · 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 P12995
- Elsewhere: RCSB PDB 1MLY · PDBe 1MLY · UniProt P12995
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