MolNFT v1 · #126804 · protein
Crystal structure of outer membrane expressed chitoporin vhchip from vibrio harveyi in complex with chitotetraose
5MDS: “Crystal structure of outer membrane expressed chitoporin vhchip from vibrio harveyi in complex with…”. X-ray diffraction, 1 ligand (NAG), 18 pockets (best druggability 0.70). MolNFT v1 #126804 on GenesisL1: 3D structure, binding…
- 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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