MolNFT v1 · #173073 · protein
Structure of the laspartomycin C friulimicin-like mutant in complex with geranyl phosphate
7ANY: “Structure of the laspartomycin C friulimicin-like mutant in complex with geranyl phosphate”. X-ray diffraction, 6 ligands (9GE, RDZ, CA), 3 pockets (best druggability 0.38). MolNFT v1 #173073 on GenesisL1: 3D structure, binding…
- PDB
- 7ANY
- Type
- protein
- Length
- 132 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laspartomycin C friulimicin-like mutant
- Ligands
- 9GE, RDZ, CA, CD, NA, CL
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Laspartomycin C friulimicin-like mutant | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- 9GE · (~{E})-13-methyltetradec-2-enoic acid · ligand · 12 copies · chains A, B, D, C, F, E, G, H, K, I, J, L
- RDZ · Geranyl phosphate · ligand · 12 copies · chains A, B, D, C, E, F, G, H, I, J, K, L
- CA · Calcium ion · metal · 42 copies · chains A, B, D, C, F, K, G, H, E, I, J, L
- CD · Cadmium ion · metal · 3 copies · chains C, D, K, B, I, J
- NA · Sodium ion · metal · chains J
- CL · Chloride ion · ion · 14 copies · chains A, B, C, K, D, E, F, G, H, I, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.38 | 0.73 | 30 | CL, CA |
| 2 | 59 | 0.31 | 0.76 | 18 | CA, RDZ |
| 3 | 57 | 0.30 | 0.76 | 17 | CA, RDZ |
Interfaces
22 interfaces between chains.
- G–K · 144 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 143 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 142 Ų buried · 3 hydrogen bonds · protein-protein
- H–I · 142 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 142 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 12 covalent (nonstandard, covalent ligand).
Compared structures
- 7ANY · Structure of the Laspartomycin C Friulimicin-like mutant in complex with Geranyl phosphate · 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 7ANY · PDBe 7ANY
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