Research workbench
Crystal structure of cysteine peptidase (NP_982244.1) from bacillus cereus atcc 10987 at 2.50 a resolution
Analyse Crystal structure of cysteine peptidase (NP_982244.1) from bacillus cereus atcc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KW0
- Type
- protein
- Length
- 773 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine peptidase
- UniProt
- Q74NK7
- Ligands
- LYS, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine peptidase | protein | 189 | 37% helix, 24% strand | Q74NK7 |
| B | Cysteine peptidase | protein | 197 | 37% helix, 23% strand | Q74NK7 |
| C | Cysteine peptidase | protein | 197 | 36% helix, 23% strand | Q74NK7 |
| D | Cysteine peptidase | protein | 190 | 38% helix, 24% strand | Q74NK7 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 9 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.76 | 0.78 | 129 | LYS, CL |
| 2 | 107 | 0.71 | 0.93 | 22 | empty |
| 3 | 256 | 0.63 | 0.81 | 33 | empty |
| 4 | 85 | 0.60 | 0.88 | 17 | CL, LYS |
| 5 | 129 | 0.47 | 0.78 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 880 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 878 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 689 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 37 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3KW0 · Crystal structure of Cysteine peptidase (NP_982244.1) from BACILLUS CEREUS ATCC 10987 at… · the same entry in another collection · chain D against D, 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 Q74NK7
- Elsewhere: RCSB PDB 3KW0 · PDBe 3KW0 · UniProt Q74NK7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.