Research workbench
Crystal structure of the metallo-beta-lactamase fold protein yhfi from bacillus subtilis (space group I4122)
Analyse Crystal structure of the metallo-beta-lactamase fold protein yhfi from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KNS
- Type
- protein
- Length
- 968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative metal-dependent hydrolase
- UniProt
- E0TYN8
- Ligands
- ZN, CA
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative metal-dependent hydrolase | protein | 246 | 21% helix, 31% strand | E0TYN8 |
| B | Putative metal-dependent hydrolase | protein | 241 | 22% helix, 32% strand | E0TYN8 |
| C | Putative metal-dependent hydrolase | protein | 241 | 22% helix, 32% strand | E0TYN8 |
| D | Putative metal-dependent hydrolase | protein | 240 | 20% helix, 30% strand | E0TYN8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.67 | 0.77 | 63 | empty |
| 2 | 129 | 0.46 | 0.78 | 23 | empty |
| 3 | 114 | 0.45 | 0.78 | 21 | empty |
| 4 | 79 | 0.41 | 0.78 | 15 | empty |
| 5 | 76 | 0.40 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 556 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 451 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6KNS · Crystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis… · 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 E0TYN8
- Elsewhere: RCSB PDB 6KNS · PDBe 6KNS · UniProt E0TYN8
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