Research workbench
Crystal structure of a chitin binding domain from burkholderia pseudomallei
Analyse Crystal structure of a chitin binding domain from burkholderia pseudomallei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UAM
- Type
- protein
- Length
- 1,181 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitin binding domain
- UniProt
- Q3JY22
- Ligands
- NO3
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chitin binding domain | protein | 198 | 15% helix, 32% strand | Q3JY22 |
| C, E | Chitin binding domain | protein | 193 | 15% helix, 29% strand | Q3JY22 |
| D | Chitin binding domain | protein | 200 | 14% helix, 28% strand | Q3JY22 |
| F | Chitin binding domain | protein | 199 | 14% helix, 28% strand | Q3JY22 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 5 copies · chains A, B, C, E
- GOL · Glycerol · additive · 3 copies · chains A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.71 | 0.75 | 87 | empty |
| 2 | 533 | 0.68 | 0.78 | 70 | empty |
| 3 | 77 | 0.59 | 0.88 | 15 | empty |
| 4 | 146 | 0.53 | 0.81 | 33 | empty |
| 5 | 213 | 0.53 | 0.77 | 28 | NO3, GOL |
Interfaces
11 interfaces between chains.
- C–F · 313 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 312 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 312 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 307 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3UAM · Crystal structure of a chitin binding domain from Burkholderia pseudomallei · 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 Q3JY22
- Elsewhere: RCSB PDB 3UAM · PDBe 3UAM · UniProt Q3JY22
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