Research workbench
Lysinoalanine synthase, durn, from duramycin biosynthesis bound to 1- DHA6ALA
Analyse Lysinoalanine synthase, durn, from duramycin biosynthesis bound to 1- DHA6ALA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C0H
- Type
- protein
- Length
- 236 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysinoalanine synthase; Gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys-BH2-gly
- Ligands
- K
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysinoalanine synthase | protein | 114 | 65% helix, 6% strand | — |
| B | Lysinoalanine synthase | protein | 108 | 68% helix, 6% strand | — |
| C | Gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys-BH2-gly | protein | 14 | 0% helix, 0% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.45 | 0.76 | 23 | empty |
| 2 | 56 | 0.36 | 0.79 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3317 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 166 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 d-amino (nonstandard, D-amino acid).
Compared structures
- 6C0H · Lysinoalanine synthase, DurN, from duramycin biosynthesis bound to 1-Dha6Ala · 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 6C0H · PDBe 6C0H
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