Research workbench
Crystal structure of in vitro folded chitoporin vhchip from vibrio harveyi in complex with chitohexaose
Analyse Crystal structure of in vitro folded chitoporin vhchip from vibrio harveyi in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MDR
- Type
- protein
- Length
- 2,046 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitoporin
- UniProt
- L0RVU0
- Ligands
- NAG, NA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Chitoporin | protein | 341 | 7% helix, 59% strand | L0RVU0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 18 copies · chains A, C, B, D, F, E
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 15 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.69 | 0.76 | 73 | NAG |
| 2 | 659 | 0.69 | 0.77 | 57 | NAG |
| 3 | 694 | 0.69 | 0.77 | 66 | NAG |
| 4 | 740 | 0.68 | 0.76 | 68 | NAG |
| 5 | 654 | 0.68 | 0.77 | 69 | NAG |
Interfaces
10 interfaces between chains.
- D–E · 1627 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1619 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1619 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1618 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1618 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 5MDR · Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi in complex… · 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 5MDR · PDBe 5MDR · UniProt L0RVU0
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