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ZG3597, a family 117 glycoside hydrolase, produced by the marine bacterium zobellia galactanivorans
Analyse ZG3597, a family 117 glycoside hydrolase, produced by the marine bacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U6B
- Type
- protein
- Length
- 1,371 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical lipoprotein
- EC
- 3.2.1.-
- UniProt
- F0V1E1
- Ligands
- CA, NA
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Conserved hypothetical lipoprotein (EC 3.2.1.-) | protein | 343 | 6% helix, 43% strand | F0V1E1 |
| C | Conserved hypothetical lipoprotein (EC 3.2.1.-) | protein | 342 | 6% helix, 44% strand | F0V1E1 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.72 | 0.95 | 24 | CA, EDO |
| 2 | 73 | 0.70 | 0.96 | 19 | CA |
| 3 | 79 | 0.70 | 0.95 | 23 | CA, EDO |
| 4 | 59 | 0.69 | 0.97 | 14 | CA |
| 5 | 494 | 0.66 | 0.78 | 80 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1910 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1798 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 798 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4U6B · Zg3597, a family 117 glycoside hydrolase, produced by the marine bacterium Zobellia… · 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 F0V1E1
- Elsewhere: RCSB PDB 4U6B · PDBe 4U6B · UniProt F0V1E1
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