Research workbench
Haloalkane dehalogenase dmxa from marinobacter sp. ELB17 possessing a unique catalytic residue
Analyse Haloalkane dehalogenase dmxa from marinobacter sp. ELB17 possessing a unique… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MXP
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA/BETA hydrolase
- EC
- 3.8.1.5
- UniProt
- A3JB27
- Ligands
- NA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ALPHA/BETA hydrolase (EC 3.8.1.5) | protein | 294 | 46% helix, 20% strand | A3JB27 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.65 | 0.82 | 51 | ACT, NA |
| 2 | 88 | 0.46 | 0.80 | 20 | empty |
| 3 | 101 | 0.46 | 0.79 | 20 | NA |
| 4 | 76 | 0.39 | 0.78 | 20 | NA |
Interfaces
1 interface between chains.
- A–B · 693 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5MXP · Haloalkane dehalogenase DmxA from Marinobacter sp. ELB17 possessing a unique catalytic… · 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 A3JB27
- Elsewhere: RCSB PDB 5MXP · PDBe 5MXP · UniProt A3JB27
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