MolNFT v1 · #63851 · protein
X-ray crystal structure of transcriptional regulator (marr family) from rhodococcus sp. RHA1
3FM5: “X-ray crystal structure of transcriptional regulator (marr family) from rhodococcus sp. RHA1”. X-ray diffraction, 2 ligands (MG, CL), 7 pockets (best druggability 0.74). MolNFT v1 #63851 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3FM5
- Type
- protein
- Length
- 546 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator
- UniProt
- Q0S6D0
- Ligands
- MG, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator | protein | 131 | 72% helix, 3% strand | Q0S6D0 |
| B | Transcriptional regulator | protein | 140 | 66% helix, 9% strand | Q0S6D0 |
| C | Transcriptional regulator | protein | 137 | 70% helix, 10% strand | Q0S6D0 |
| D | Transcriptional regulator | protein | 138 | 69% helix, 9% strand | Q0S6D0 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · chains D
- GOL · Glycerol · additive · 2 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.74 | 0.79 | 80 | GOL |
| 2 | 296 | 0.63 | 0.80 | 39 | GOL, EDO |
| 3 | 148 | 0.54 | 0.81 | 25 | empty |
| 4 | 158 | 0.51 | 0.79 | 22 | empty |
| 5 | 95 | 0.46 | 0.80 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2267 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 2219 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 280 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 249 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 3FM5 · X-ray crystal structure of transcriptional regulator (MarR family) from Rhodococcus sp.… · 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 Q0S6D0
- Elsewhere: RCSB PDB 3FM5 · PDBe 3FM5 · UniProt Q0S6D0
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