MolNFT v1 · #126803 · protein
Crystal structure of in vitro folded chitoporin vhchip from vibrio harveyi in complex with chitohexaose
5MDR: “Crystal structure of in vitro folded chitoporin vhchip from vibrio harveyi in complex with chitohexaose”. X-ray diffraction, 2 ligands (NAG, NA), 20 pockets (best druggability 0.69). MolNFT v1 #126803 on GenesisL1: 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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