MolNFT v1 · #27238 · protein
Crystal structure of aclacinomycin-10-hydroxylase (rdmb) in complex with S-adenosyl-L-methionine (SAM) and 11-deoxy- beta-rhodomycin (dbra)
1XDS · Protein rdmb: “Crystal structure of aclacinomycin-10-hydroxylase (rdmb) in complex with S-adenosyl-L-methionine (SAM) and…”. X-ray diffraction, 2 ligands (SAM, DRA), 6 pockets (best druggability 0.83). MolNFT v1 #27238 on GenesisL1…
- PDB
- 1XDS
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein rdmb
- UniProt
- Q54527
- Ligands
- SAM, DRA
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein rdmb | protein | 336 | 49% helix, 17% strand | Q54527 |
| B | Protein rdmb | protein | 330 | 48% helix, 16% strand | Q54527 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- DRA · 11-deoxy-beta-rhodomycin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.83 | 0.85 | 73 | SAM, DRA |
| 2 | 941 | 0.82 | 0.83 | 80 | SAM, DRA |
| 3 | 195 | 0.52 | 0.78 | 27 | empty |
| 4 | 122 | 0.52 | 0.82 | 17 | empty |
| 5 | 85 | 0.34 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3724 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1XDS · Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q54527 · AlphaFold monomer V2.0 prediction for aclacinomycin 10-hydroxylase rdmb (Q54527) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q54527
- Elsewhere: RCSB PDB 1XDS · PDBe 1XDS · UniProt Q54527
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