Research workbench
Structure of ester-hydrolase EH1AB1 from the metagenome of lake arreo complexed with a derivative of bipyridine phosphonate
Analyse Structure of ester-hydrolase EH1AB1 from the metagenome of lake arreo complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RKY
- Type
- protein
- Length
- 1,260 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EH1AB1
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | EH1AB1 | protein | 315 | 41% helix, 20% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.76 | 0.79 | 94 | empty |
| 2 | 821 | 0.76 | 0.80 | 79 | empty |
| 3 | 295 | 0.67 | 0.82 | 35 | empty |
| 4 | 283 | 0.64 | 0.81 | 33 | empty |
| 5 | 69 | 0.56 | 0.88 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 980 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 976 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 514 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6RKY · Structure of ester-hydrolase EH1AB1 from the metagenome of lake arreo complexed with a… · 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 6RKY · PDBe 6RKY
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