MolNFT v1 · #189700 · protein
Crystal structure of chitinase-H from O. furnacalis in complex with lynamicin B
7VRG: “Crystal structure of chitinase-H from O. furnacalis in complex with lynamicin B”. X-ray diffraction, 2 ligands (7U8, NAG), 5 pockets (best druggability 0.79). MolNFT v1 #189700 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7VRG
- Type
- protein
- Length
- 1,080 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase
- UniProt
- Q4AE59
- Ligands
- 7U8, NAG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chitinase | protein | 540 | 29% helix, 26% strand | Q4AE59 |
Ligands and binding sites
- 7U8 · methyl 4-[5,6-bis(chloranyl)-1H-indol-3-yl]-3-(5-chloranyl-1H-indol-3-yl)-1H-pyrrole-2-carboxylate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.79 | 0.80 | 117 | 7U8 |
| 2 | 630 | 0.72 | 0.79 | 65 | 7U8 |
| 3 | 135 | 0.42 | 0.76 | 22 | empty |
| 4 | 133 | 0.39 | 0.74 | 23 | empty |
| 5 | 50 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 529 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 7VRG · Crystal structure of chitinase-h from O. furnacalis in complex with Lynamicin B · 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 Q4AE59
- Elsewhere: RCSB PDB 7VRG · PDBe 7VRG · UniProt Q4AE59
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