Research workbench
Crystal structure of putative ancestral haloalkane dehalogenase AncHLD2 (node 2)
Analyse Crystal structure of putative ancestral haloalkane dehalogenase AncHLD2 (node 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y9E
- Type
- protein
- Length
- 1,741 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- synthetic construct
- Molecule
- Ancestral haloalkane dehalogenase AncHLD2
- Ligands
- CL
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.7 · 4 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ancestral haloalkane dehalogenase AncHLD2 | protein | 291 | 47% helix, 21% strand | — |
| D | Ancestral haloalkane dehalogenase AncHLD2 | protein | 291 | 46% helix, 21% strand | — |
| E | Ancestral haloalkane dehalogenase AncHLD2 | protein | 287 | 48% helix, 21% strand | — |
| F | Ancestral haloalkane dehalogenase AncHLD2 | protein | 290 | 46% helix, 21% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, C, B, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.81 | 0.86 | 89 | EDO |
| 2 | 263 | 0.66 | 0.83 | 49 | empty |
| 3 | 243 | 0.64 | 0.82 | 35 | EDO |
| 4 | 125 | 0.57 | 0.83 | 28 | CL, EDO |
| 5 | 104 | 0.56 | 0.84 | 26 | CL, MPD |
Interfaces
8 interfaces between chains.
- A–B · 604 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 196 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 162 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Y9E · Crystal structure of putative ancestral haloalkane dehalogenase ANCHLD2 (node 2) · 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
- Elsewhere: RCSB PDB 6Y9E · PDBe 6Y9E
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.