Research workbench
Crystal structure of outer membrane expressed chitoporin vhchip from vibrio harveyi
Analyse Crystal structure of outer membrane expressed chitoporin vhchip from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MDQ
- Type
- protein
- Length
- 1,050 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitoporin
- UniProt
- L0RVU0
- Ligands
- NA
- Pockets
- 17 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chitoporin | protein | 350 | 7% helix, 57% strand | L0RVU0 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.67 | 0.77 | 69 | NA |
| 2 | 430 | 0.65 | 0.78 | 60 | NA |
| 3 | 477 | 0.64 | 0.77 | 45 | empty |
| 4 | 465 | 0.63 | 0.77 | 46 | empty |
| 5 | 371 | 0.62 | 0.78 | 48 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2412 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 2398 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2389 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5MDQ · Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi · the same entry in another collection · chain C against C, 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 5MDQ · PDBe 5MDQ · UniProt L0RVU0
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