MolNFT v1 · #186315 · protein
Crystal structure of a dehydrating condensation domain, ambe-cmodaa, involved in nonribosomal peptide synthesis
7R9X: “Crystal structure of a dehydrating condensation domain, ambe-cmodaa, involved in nonribosomal peptide…”. X-ray diffraction, 2 ligands (NA, IOD), 11 pockets (best druggability 0.79). MolNFT v1 #186315 on GenesisL1: 3D structure…
- PDB
- 7R9X
- Type
- protein
- Length
- 821 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ambe
- UniProt
- Q9I1H3
- Ligands
- NA, IOD
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ambe | protein | 418 | 40% helix, 23% strand | Q9I1H3 |
| B | Ambe | protein | 403 | 40% helix, 24% strand | Q9I1H3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.79 | 0.80 | 79 | IOD, NA |
| 2 | 1033 | 0.78 | 0.80 | 81 | empty |
| 3 | 81 | 0.61 | 0.89 | 19 | empty |
| 4 | 172 | 0.49 | 0.77 | 32 | empty |
| 5 | 159 | 0.46 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 120 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7R9X · Crystal structure of a dehydrating condensation domain, AmbE-CmodAA, involved in… · 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 Q9I1H3
- Elsewhere: RCSB PDB 7R9X · PDBe 7R9X · UniProt Q9I1H3
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