Research workbench
Haloalkane dehalogenase dmra from mycobacterium rhodesiae JS60
Analyse Haloalkane dehalogenase dmra from mycobacterium rhodesiae JS60 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MJ3
- Type
- protein
- Length
- 1,211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- G4I2J6
- Ligands
- K, CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 302 | 42% helix, 15% strand | G4I2J6 |
| B, C, D | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 303 | 43% helix, 15% strand | G4I2J6 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.78 | 0.90 | 50 | CL |
| 2 | 578 | 0.74 | 0.81 | 77 | CL |
| 3 | 306 | 0.68 | 0.83 | 44 | CL |
| 4 | 281 | 0.68 | 0.83 | 43 | CL |
| 5 | 374 | 0.60 | 0.76 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 770 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 362 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 350 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 267 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4MJ3 · Haloalkane dehalogenase DmrA from Mycobacterium rhodesiae JS60 · 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 G4I2J6
- Elsewhere: RCSB PDB 4MJ3 · PDBe 4MJ3 · UniProt G4I2J6
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