Research workbench
Crystal structure of holo-OBIF1, a five domain nonribosomal peptide synthetase from burkholderia diffusa
Analyse Crystal structure of holo-OBIF1, a five domain nonribosomal peptide synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N8E
- Type
- protein
- Length
- 1,332 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo-OBIF1
- Ligands
- PNS, KFG, KFJ, PO4, CL
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holo-OBIF1 | protein | 1332 | 36% helix, 21% strand | — |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · chains A
- KFG · dimethyl hydrogen phosphate · ligand · chains A
- KFJ · 4-(4-nitrophenyl)-L-threonine · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.88 | 0.92 | 68 | PNS |
| 2 | 1110 | 0.83 | 0.84 | 154 | KFJ |
| 3 | 410 | 0.73 | 0.84 | 36 | empty |
| 4 | 962 | 0.72 | 0.76 | 73 | empty |
| 5 | 136 | 0.64 | 0.87 | 24 | empty |
Modifications
Observed in the structure: 1 cofactor (phosphopantetheinylation).
Compared structures
- 6N8E · Crystal structure of holo-ObiF1, a five domain nonribosomal peptide synthetase from… · 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
- Elsewhere: RCSB PDB 6N8E · PDBe 6N8E
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