Research workbench
Apo truncated vhchip (delta 1-19)
Analyse Apo truncated vhchip (delta 1-19) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EQM
- Type
- protein
- Length
- 993 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitoporin
- UniProt
- L0RVU0
- Ligands
- NA, MG
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chitoporin | protein | 331 | 6% helix, 60% strand | L0RVU0 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.72 | 0.76 | 122 | NA, MG |
| 2 | 815 | 0.70 | 0.76 | 89 | NA |
| 3 | 802 | 0.69 | 0.76 | 68 | empty |
| 4 | 168 | 0.46 | 0.76 | 27 | empty |
| 5 | 180 | 0.46 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1353 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1341 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1330 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7EQM · Apo Truncated VhChiP (Delta 1-19) · 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 L0RVU0
- Elsewhere: RCSB PDB 7EQM · PDBe 7EQM · UniProt L0RVU0
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