Research workbench
Crystal structure of bacillus subtilis codw, a non-canonical hslv-like peptidase with an impaired catalytic apparatus
Analyse Crystal structure of bacillus subtilis codw, a non-canonical hslv-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z3B
- Type
- protein
- Length
- 2,160 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent protease hslv
- EC
- 3.4.25.-
- UniProt
- P39070
- Ligands
- NA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | ATP-dependent protease hslv (EC 3.4.25.-) | protein | 180 | 37% helix, 27% strand | P39070 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, J, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.74 | 0.77 | 130 | empty |
| 2 | 600 | 0.72 | 0.80 | 81 | empty |
| 3 | 422 | 0.72 | 0.82 | 47 | empty |
| 4 | 450 | 0.69 | 0.80 | 62 | empty |
| 5 | 393 | 0.63 | 0.78 | 41 | empty |
Interfaces
19 interfaces between chains.
- H–I · 940 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 927 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 918 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 912 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 906 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2Z3B · Crystal Structure of Bacillus Subtilis CodW, a non-canonical HslV-like peptidase with an… · the same entry in another collection · chain L against L, 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 P39070
- Elsewhere: RCSB PDB 2Z3B · PDBe 2Z3B · UniProt P39070
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