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Crystal structure of a putative sulfatase (NP_810509.1) from bacteroides thetaiotaomicron vpi-5482 at 2.40 a resolution
Analyse Crystal structure of a putative sulfatase (NP_810509.1) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B5Q
- Type
- protein
- Length
- 931 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sulfatase yidj
- UniProt
- Q8A7C8
- Ligands
- ZN, CL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sulfatase yidj | protein | 464 | 34% helix, 15% strand | Q8A7C8 |
| B | Putative sulfatase yidj | protein | 467 | 36% helix, 14% strand | Q8A7C8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.69 | 0.77 | 70 | EDO, EPE |
| 2 | 257 | 0.56 | 0.77 | 29 | empty |
| 3 | 157 | 0.51 | 0.79 | 28 | CL |
| 4 | 123 | 0.47 | 0.78 | 19 | empty |
| 5 | 159 | 0.46 | 0.76 | 29 | EPE |
Interfaces
1 interface between chains.
- A–B · 302 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3B5Q · Crystal structure of a putative sulfatase (NP_810509.1) from Bacteroides thetaiotaomicron… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8A7C8 · AlphaFold monomer V2.0 prediction for delta 4,5-hexuronate-2-O-sulfatase (Q8A7C8) · a predicted model of the same protein · 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 Q8A7C8
- Elsewhere: RCSB PDB 3B5Q · PDBe 3B5Q · UniProt Q8A7C8
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