MolNFT v1 · #25656 · protein
Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(L-arg-L-pro) at 1.85 a resolution
1W1V: “Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor…”. X-ray diffraction, 2 ligands (ALJ, SO4), 4 pockets (best druggability 0.80). MolNFT v1 #25656 on GenesisL1: 3D structure, binding sites…
- PDB
- 1W1V
- Type
- protein
- Length
- 993 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase B
- EC
- 3.2.1.14
- UniProt
- Q54276
- Ligands
- ALJ, SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase B (EC 3.2.1.14) | protein | 496 | 32% helix, 20% strand | Q54276 |
| B | Chitinase B (EC 3.2.1.14) | protein | 497 | 32% helix, 20% strand | Q54276 |
Ligands and binding sites
- ALJ · Cyclo-(L-arginine-L-proline) inhibitor · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 31 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.80 | 0.81 | 103 | GOL, ALJ |
| 2 | 1145 | 0.79 | 0.80 | 91 | GOL, SO4, ALJ |
| 3 | 85 | 0.37 | 0.77 | 21 | GOL |
| 4 | 62 | 0.28 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1437 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1W1V · Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide… · the same entry in another collection · chain B against B, 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 Q54276
- Elsewhere: RCSB PDB 1W1V · PDBe 1W1V · UniProt Q54276
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