Research workbench
Yfit from bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology
Analyse Yfit from bacillus subtilis is a probable metal-dependent hydrolase with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RXQ
- Type
- protein
- Length
- 698 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfit
- Ligands
- NI
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Yfit | protein | 174 | 64% helix, 5% strand | — |
| B | Yfit | protein | 175 | 64% helix, 5% strand | — |
| D | Yfit | protein | 175 | 64% helix, 6% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.54 | 0.75 | 32 | NI |
| 2 | 254 | 0.53 | 0.75 | 30 | empty |
| 3 | 232 | 0.52 | 0.76 | 30 | NI |
| 4 | 188 | 0.45 | 0.74 | 30 | empty |
| 5 | 84 | 0.39 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1561 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1533 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 374 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1RXQ · YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual… · 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
- Elsewhere: RCSB PDB 1RXQ · PDBe 1RXQ
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