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Crystal structure of catalytic domain of chitinase from ralstonia sp. a-471 (E141Q) in complex with tetrasaccharide
Analyse Crystal structure of catalytic domain of chitinase from ralstonia sp. a-471… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W6D
- Type
- protein
- Length
- 612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme-like chitinolytic enzyme
- EC
- 3.2.1.14
- UniProt
- B7XCV4
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysozyme-like chitinolytic enzyme (EC 3.2.1.14) | protein | 153 | 59% helix, 1% strand | B7XCV4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.73 | 0.81 | 51 | NAG |
| 2 | 633 | 0.71 | 0.79 | 52 | NAG |
| 3 | 516 | 0.63 | 0.76 | 49 | NAG |
| 4 | 251 | 0.55 | 0.77 | 38 | NAG |
| 5 | 118 | 0.46 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–D · 494 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 292 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3W6D · Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 (E141Q) in… · 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 B7XCV4
- Elsewhere: RCSB PDB 3W6D · PDBe 3W6D · UniProt B7XCV4
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