Research workbench
X-ray crystal structure of a putative AMIDOHYDROLASE/PEPTIDASE from burkholderia cenocepacia
Analyse X-ray crystal structure of a putative AMIDOHYDROLASE/PEPTIDASE from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WJB
- Type
- protein
- Length
- 1,628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative AMIDOHYDROLASE/PEPTIDASE
- EC
- 3.5.1.87
- UniProt
- B4EHA1
- Ligands
- ZN, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative AMIDOHYDROLASE/PEPTIDASE (EC 3.5.1.87) | protein | 409 | 37% helix, 24% strand | B4EHA1 |
| B, C | Putative AMIDOHYDROLASE/PEPTIDASE (EC 3.5.1.87) | protein | 407 | 36% helix, 24% strand | B4EHA1 |
| D | Putative AMIDOHYDROLASE/PEPTIDASE (EC 3.5.1.87) | protein | 405 | 36% helix, 23% strand | B4EHA1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.78 | 0.86 | 91 | SO4 |
| 2 | 751 | 0.78 | 0.82 | 99 | EDO, SO4 |
| 3 | 399 | 0.61 | 0.77 | 50 | EDO |
| 4 | 365 | 0.58 | 0.76 | 45 | SO4 |
| 5 | 93 | 0.44 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2140 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2127 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1012 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4WJB · X-ray crystal structure of a putative amidohydrolase/peptidase from Burkholderia… · 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 B4EHA1
- Elsewhere: RCSB PDB 4WJB · PDBe 4WJB · UniProt B4EHA1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.