Research workbench
Lysinoalanine synthase, durn, from duramycin biosynthesis bound to duramycin
Analyse Lysinoalanine synthase, durn, from duramycin biosynthesis bound to duramycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C0Y
- Type
- protein
- Length
- 1,009 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysinoalanine synthase; Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys…
- Ligands
- K
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysinoalanine synthase | protein | 107 | 67% helix, 7% strand | — |
| C, D, E, F, G, H | Lysinoalanine synthase | protein | 108 | 67% helix, 6% strand | — |
| O, I, J, K, N, P | Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys- BH2-gly-asn-dbb-lys | protein | 19 | 0% helix, 21% strand | — |
| L | Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys- BH2-gly-asn-dbb-lys | protein | 18 | 0% helix, 11% strand | — |
| M | Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys- BH2-gly-asn-dbb-lys | protein | 15 | 0% helix, 0% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.74 | 0.82 | 67 | empty |
| 2 | 831 | 0.73 | 0.78 | 68 | empty |
| 3 | 610 | 0.72 | 0.79 | 62 | empty |
| 4 | 599 | 0.68 | 0.77 | 53 | empty |
| 5 | 106 | 0.44 | 0.79 | 19 | empty |
Interfaces
37 interfaces between chains.
- C–G · 3277 Ų buried · 45 hydrogen bonds · protein-protein
- D–H · 3256 Ų buried · 44 hydrogen bonds · protein-protein
- A–E · 3219 Ų buried · 45 hydrogen bonds · protein-protein
- B–F · 3196 Ų buried · 43 hydrogen bonds · protein-protein
- C–O · 604 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified, 8 d-amino (nonstandard, D-amino acid).
Compared structures
- 6C0Y · Lysinoalanine synthase, DurN, from duramycin biosynthesis bound to duramycin · 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 6C0Y · PDBe 6C0Y
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