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Crystal structure of had family enzyme bt-2542 (target efi-501088) from bacteroides thetaiotaomicron, magnesium complex
Analyse Crystal structure of had family enzyme bt-2542 (target efi-501088) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DFD
- Type
- protein
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative haloacid dehalogenase-like hydrolase
- UniProt
- Q8A4Q5
- Ligands
- UNL, MG, CL
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative haloacid dehalogenase-like hydrolase | protein | 205 | 47% helix, 13% strand | Q8A4Q5 |
| B | Putative haloacid dehalogenase-like hydrolase | protein | 198 | 49% helix, 14% strand | Q8A4Q5 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.79 | 0.80 | 73 | MG, CL |
| 2 | 52 | 0.34 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 665 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4DFD · Crystal structure of had family enzyme bt-2542 (target efi-501088) from bacteroides… · 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 Q8A4Q5
- Elsewhere: RCSB PDB 4DFD · PDBe 4DFD · UniProt Q8A4Q5
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