Research workbench
Crystal structure of outer membrane expressed chitoporin vhchip from vibrio harveyi in complex with chitotetraose
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
- 5MDS
- Type
- protein
- Length
- 1,023 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitoporin
- UniProt
- L0RVU0
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chitoporin | protein | 341 | 7% helix, 59% strand | L0RVU0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.70 | 0.76 | 83 | NAG |
| 2 | 715 | 0.69 | 0.77 | 76 | NAG |
| 3 | 759 | 0.68 | 0.76 | 72 | NAG |
| 4 | 195 | 0.49 | 0.76 | 29 | empty |
| 5 | 204 | 0.48 | 0.75 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1670 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1655 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1654 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5MDS · Crystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi in… · 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 5MDS · PDBe 5MDS · UniProt L0RVU0
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