MolNFT v1 · #154571 · protein
Amino-transferase (amt) domain of hybrid POLYKETIDE/NON-ribosomal peptide synthetase
6KFM · Mycosubtilin synthase subunit a: “Amino-transferase (amt) domain of hybrid POLYKETIDE/NON-ribosomal peptide synthetase”. X-ray diffraction, 1 ligand (PLP), 6 pockets (best druggability 0.78). MolNFT v1 #154571 on GenesisL1: 3D…
- PDB
- 6KFM
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycosubtilin synthase subunit a
- EC
- 2.3.1.-
- UniProt
- Q9R9J1
- Ligands
- PLP
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mycosubtilin synthase subunit a (EC 2.3.1.-) | protein | 449 | 46% helix, 17% strand | Q9R9J1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.78 | 0.96 | 24 | empty |
| 2 | 146 | 0.78 | 0.95 | 31 | empty |
| 3 | 494 | 0.73 | 0.82 | 71 | GOL, PLP |
| 4 | 62 | 0.71 | 0.98 | 20 | empty |
| 5 | 63 | 0.70 | 0.97 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 5235 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6KFM · Amino-transferase (AMT) Domain of Hybrid Polyketide/Non-Ribosomal Peptide Synthetase · 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 Q9R9J1
- Elsewhere: RCSB PDB 6KFM · PDBe 6KFM · UniProt Q9R9J1
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