Research workbench
Crystal structure of phenylurea hydrolase B
Analyse Crystal structure of phenylurea hydrolase B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WHB
- Type
- protein
- Length
- 3,672 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylurea hydrolase B
- UniProt
- B8R4K0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, B, C, D, F, G, H | Phenylurea hydrolase B | protein | 459 | 34% helix, 16% strand | B8R4K0 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.76 | 0.85 | 50 | empty |
| 2 | 449 | 0.76 | 0.85 | 59 | empty |
| 3 | 78 | 0.76 | 0.98 | 16 | empty |
| 4 | 1059 | 0.76 | 0.78 | 88 | empty |
| 5 | 513 | 0.76 | 0.83 | 60 | empty |
Interfaces
12 interfaces between chains.
- E–D · 947 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 939 Ų buried · 18 hydrogen bonds · protein-protein
- B–G · 919 Ų buried · 16 hydrogen bonds · protein-protein
- C–H · 870 Ų buried · 17 hydrogen bonds · protein-protein
- A–G · 290 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4WHB · Crystal structure of phenylurea hydrolase B · the same entry in another collection · chain E against E, 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 B8R4K0
- Elsewhere: RCSB PDB 4WHB · PDBe 4WHB · UniProt B8R4K0
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