Research workbench
Crystal structure of catalytic domain of chitinase from ralstonia sp. a-471 (E162Q) in complex with disaccharide
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
- 3W6F
- Type
- protein
- Length
- 607 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
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme-like chitinolytic enzyme (EC 3.2.1.14) | protein | 150 | 61% helix, 1% strand | B7XCV4 |
| B, D | Lysozyme-like chitinolytic enzyme (EC 3.2.1.14) | protein | 153 | 59% helix, 1% strand | B7XCV4 |
| C | Lysozyme-like chitinolytic enzyme (EC 3.2.1.14) | protein | 151 | 58% helix, 1% strand | B7XCV4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.69 | 0.81 | 43 | NAG |
| 2 | 554 | 0.68 | 0.78 | 52 | NAG |
| 3 | 639 | 0.67 | 0.76 | 61 | NAG |
| 4 | 255 | 0.55 | 0.77 | 38 | NAG |
| 5 | 99 | 0.44 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 478 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 270 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3W6F · Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 (E162Q) 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 3W6F · PDBe 3W6F · UniProt B7XCV4
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