Research workbench
Structure of EAL Enzyme Bd1971 - halfsite-occupied form
Analyse Structure of EAL Enzyme Bd1971 - halfsite-occupied form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HQ3
- Type
- protein
- Length
- 434 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.79
- Source
- Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
- Molecule
- EAL Enzyme Bd1971
- UniProt
- Q6MLN6
- Ligands
- CMP
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.79 · 3 distinct chains · 29% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EAL Enzyme Bd1971 | protein | 111 | 30% helix, 38% strand | Q6MLN6 |
| B, D | EAL Enzyme Bd1971 | protein | 107 | 26% helix, 39% strand | Q6MLN6 |
| C | EAL Enzyme Bd1971 | protein | 109 | 30% helix, 39% strand | Q6MLN6 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.81 | 0.82 | 90 | empty |
| 2 | 209 | 0.62 | 0.82 | 28 | CMP |
| 3 | 185 | 0.60 | 0.82 | 28 | CMP |
| 4 | 81 | 0.36 | 0.75 | 17 | empty |
| 5 | 66 | 0.34 | 0.76 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1346 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1300 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 383 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 379 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6HQ3 · Structure of eal enzyme BD1971 - halfsite-occupied form · 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 Q6MLN6
- Elsewhere: RCSB PDB 6HQ3 · PDBe 6HQ3 · UniProt Q6MLN6
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