Research workbench
Crystal structure of a cystatin-like protein (BACCAC_01506) from bacteroides caccae atcc 43185 at 1.69 a resolution
Analyse Crystal structure of a cystatin-like protein (BACCAC_01506) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R4K
- Type
- protein
- Length
- 602 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A5ZF42
- Ligands
- PEU, CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein | protein | 151 | 28% helix, 31% strand | A5ZF42 |
| B | Uncharacterized protein | protein | 152 | 28% helix, 32% strand | A5ZF42 |
| D | Uncharacterized protein | protein | 148 | 31% helix, 34% strand | A5ZF42 |
Ligands and binding sites
- PEU · 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, 59,62,65,68,71,74,77,80-heptacosaoxadooctacontan-82-ol · ligand · 13 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, C
- ACT · Acetate ion · additive · 4 copies · chains A, D
- GOL · Glycerol · additive · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.77 | 0.81 | 84 | PEU |
| 2 | 446 | 0.64 | 0.77 | 58 | PEU |
| 3 | 231 | 0.57 | 0.79 | 29 | GOL |
| 4 | 177 | 0.54 | 0.79 | 36 | empty |
| 5 | 118 | 0.50 | 0.81 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 750 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 676 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 582 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 286 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 211 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4R4K · Crystal structure of a cystatin-like protein (BACCAC_01506) from Bacteroides caccae ATCC… · 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 A5ZF42
- Elsewhere: RCSB PDB 4R4K · PDBe 4R4K · UniProt A5ZF42
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