MolNFT v1 · #173312 · protein
The tetrameric structure of haloalkane dehalogenase dpaa from paraglaciecola agarilytica NO2
7AVR · Haloalkane dehalogenase 1: “The tetrameric structure of haloalkane dehalogenase dpaa from paraglaciecola agarilytica NO2”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.86). MolNFT v1 #173312 on GenesisL1: 3D…
- PDB
- 7AVR
- Type
- protein
- Length
- 2,387 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase 1
- EC
- 3.8.1.5
- UniProt
- K6XNL5
- Ligands
- CL
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Haloalkane dehalogenase 1 (EC 3.8.1.5) | protein | 299 | 40% helix, 17% strand | K6XNL5 |
| B, E | Haloalkane dehalogenase 1 (EC 3.8.1.5) | protein | 298 | 42% helix, 17% strand | K6XNL5 |
| C, G | Haloalkane dehalogenase 1 (EC 3.8.1.5) | protein | 299 | 41% helix, 17% strand | K6XNL5 |
| D | Haloalkane dehalogenase 1 (EC 3.8.1.5) | protein | 297 | 42% helix, 17% strand | K6XNL5 |
| F | Haloalkane dehalogenase 1 (EC 3.8.1.5) | protein | 298 | 42% helix, 17% strand | K6XNL5 |
Ligands and binding sites
- CL · Chloride ion · ion · 18 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.86 | 0.88 | 127 | CL |
| 2 | 478 | 0.80 | 0.87 | 48 | CL |
| 3 | 463 | 0.79 | 0.87 | 46 | CL |
| 4 | 643 | 0.79 | 0.84 | 57 | CL |
| 5 | 473 | 0.78 | 0.86 | 49 | CL |
Interfaces
14 interfaces between chains.
- E–H · 1003 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 982 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 968 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 962 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 661 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7AVR · The tetrameric structure of haloalkane dehalogenase DpaA from Paraglaciecola agarilytica… · 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 K6XNL5
- Elsewhere: RCSB PDB 7AVR · PDBe 7AVR · UniProt K6XNL5
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