MolNFT v1 · #81297 · protein
Crystal structure of the defluorinating L-2-haloacid dehalogenase RHA0230
3UMG: “Crystal structure of the defluorinating L-2-haloacid dehalogenase RHA0230”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.77). MolNFT v1 #81297 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UMG
- Type
- protein
- Length
- 1,971 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloacid dehalogenase
- EC
- 3.8.1.2
- UniProt
- Q0SK70
- Ligands
- CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloacid dehalogenase (EC 3.8.1.2) | protein | 247 | 49% helix, 11% strand | Q0SK70 |
| B | Haloacid dehalogenase (EC 3.8.1.2) | protein | 247 | 49% helix, 12% strand | Q0SK70 |
| C, F | Haloacid dehalogenase (EC 3.8.1.2) | protein | 245 | 47% helix, 11% strand | Q0SK70 |
| D | Haloacid dehalogenase (EC 3.8.1.2) | protein | 248 | 49% helix, 10% strand | Q0SK70 |
| E | Haloacid dehalogenase (EC 3.8.1.2) | protein | 248 | 50% helix, 11% strand | Q0SK70 |
| G | Haloacid dehalogenase (EC 3.8.1.2) | protein | 246 | 50% helix, 11% strand | Q0SK70 |
| H | Haloacid dehalogenase (EC 3.8.1.2) | protein | 245 | 50% helix, 11% strand | Q0SK70 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.77 | 0.80 | 92 | empty |
| 2 | 770 | 0.66 | 0.74 | 60 | empty |
| 3 | 768 | 0.65 | 0.74 | 61 | empty |
| 4 | 264 | 0.56 | 0.77 | 29 | empty |
| 5 | 350 | 0.55 | 0.75 | 35 | empty |
Interfaces
12 interfaces between chains.
- E–F · 778 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 776 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 765 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 764 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 449 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UMG · Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase Rha0230 · 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 Q0SK70
- Elsewhere: RCSB PDB 3UMG · PDBe 3UMG · UniProt Q0SK70
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