Research workbench
Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_470671.1) from listeria innocua at 2.12 a resolution
Analyse Crystal structure of putative cystathionine beta-lyase involved in aluminum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FD0
- Type
- protein
- Length
- 816 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cystathionine beta-lyase involved in aluminum resistance
- UniProt
- Q92C56
- Ligands
- CA
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative cystathionine beta-lyase involved in aluminum resistance | protein | 408 | 43% helix, 15% strand | Q92C56 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 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 | 666 | 0.72 | 0.79 | 65 | EDO |
| 2 | 648 | 0.71 | 0.79 | 54 | EDO |
| 3 | 78 | 0.66 | 0.92 | 20 | PGE |
| 4 | 68 | 0.42 | 0.81 | 19 | empty |
| 5 | 61 | 0.41 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2121 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered, cofactor).
Compared structures
- 3FD0 · Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance… · 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 Q92C56
- Elsewhere: RCSB PDB 3FD0 · PDBe 3FD0 · UniProt Q92C56
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