Research workbench
RHCC in complex with Naphthalene
Analyse RHCC in complex with Naphthalene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VKF
- Type
- protein
- Length
- 208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.752
- Source
- Staphylothermus marinus
- Molecule
- Tetrabrachion
- UniProt
- Q54436
- Ligands
- NPY, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.752 · 1 distinct chain · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tetrabrachion | protein | 52 | 92% helix, 0% strand | Q54436 |
Ligands and binding sites
- NPY · Naphthalene · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.81 | 0.99 | 18 | NPY |
| 2 | 122 | 0.81 | 0.98 | 19 | NPY |
| 3 | 84 | 0.76 | 0.98 | 18 | empty |
| 4 | 92 | 0.67 | 0.91 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1127 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1120 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1107 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1060 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5VKF · Rhcc in complex with naphthalene · 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 Q54436
- Elsewhere: RCSB PDB 5VKF · PDBe 5VKF · UniProt Q54436
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