MolNFT v1 · #88850 · protein
Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (rosa) from streptomyces davawensis
4D7K · SAM-dependent methyltransferases: “Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (rosa) from streptomyces…”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #88850 on GenesisL1: 3D…
- PDB
- 4D7K
- Type
- protein
- Length
- 2,013 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferases
- EC
- 2.1.1.-
- UniProt
- K4RFM2
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | SAM-dependent methyltransferases (EC 2.1.1.-) | protein | 335 | 50% helix, 17% strand | K4RFM2 |
| D | SAM-dependent methyltransferases (EC 2.1.1.-) | protein | 336 | 51% helix, 17% strand | K4RFM2 |
| F | SAM-dependent methyltransferases (EC 2.1.1.-) | protein | 337 | 50% helix, 17% strand | K4RFM2 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.77 | 0.81 | 60 | empty |
| 2 | 748 | 0.77 | 0.81 | 57 | empty |
| 3 | 782 | 0.76 | 0.80 | 61 | empty |
| 4 | 782 | 0.76 | 0.80 | 77 | empty |
| 5 | 839 | 0.75 | 0.79 | 70 | empty |
Interfaces
8 interfaces between chains.
- C–D · 3566 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 3503 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3502 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 357 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 340 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4D7K · Crystal structure of N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) from… · the same entry in another collection · chain F against F, TM-score 1.00
- K4RFM2 · AlphaFold monomer V2.0 prediction for 8-amino-8-demethylriboflavin… · a predicted model of the same protein · chain D against A, TM-score 0.95
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 K4RFM2
- Elsewhere: RCSB PDB 4D7K · PDBe 4D7K · UniProt K4RFM2
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