MolNFT v1 · #66629 · protein
Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from clostridium acetobutylicum at 2.00 a resolution
3HVY · Cystathionine beta-lyase family protein, ynbb B.SUBTILIS…: “Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from…”. X-ray diffraction, 1 ligand (NA), 18 pockets (best druggability…
- PDB
- 3HVY
- Type
- protein
- Length
- 1,677 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathionine beta-lyase family protein, ynbb B.SUBTILIS ortholog
- UniProt
- Q97I22
- Ligands
- NA
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cystathionine beta-lyase family protein, ynbb B.SUBTILIS ortholog | protein | 417 | 45% helix, 14% strand | Q97I22 |
| C | Cystathionine beta-lyase family protein, ynbb B.SUBTILIS ortholog | protein | 420 | 45% helix, 14% strand | Q97I22 |
| D | Cystathionine beta-lyase family protein, ynbb B.SUBTILIS ortholog | protein | 423 | 44% helix, 14% strand | Q97I22 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.85 | 0.88 | 66 | empty |
| 2 | 1073 | 0.79 | 0.81 | 123 | empty |
| 3 | 766 | 0.72 | 0.78 | 89 | empty |
| 4 | 523 | 0.72 | 0.81 | 39 | EDO |
| 5 | 531 | 0.72 | 0.80 | 46 | EDO |
Interfaces
6 interfaces between chains.
- B–D · 2586 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2510 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2134 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2127 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 278 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered, cofactor).
Compared structures
- 3HVY · 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 Q97I22
- Elsewhere: RCSB PDB 3HVY · PDBe 3HVY · UniProt Q97I22
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