Research workbench
Crystal structure of the anti-sigma factor rsiv bound to lysozyme
Analyse Crystal structure of the anti-sigma factor rsiv bound to lysozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JEN
- Type
- protein
- Length
- 673 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-sigma-V factor rsiv; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- O05403, P00698
- Ligands
- NA, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-sigma-V factor rsiv | protein | 210 | 27% helix, 35% strand | O05403 |
| B, D | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
| C | Anti-sigma-V factor rsiv | protein | 205 | 27% helix, 36% strand | O05403 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.73 | 0.76 | 71 | empty |
| 2 | 155 | 0.51 | 0.79 | 19 | empty |
| 3 | 140 | 0.46 | 0.77 | 20 | empty |
| 4 | 74 | 0.44 | 0.81 | 16 | empty |
| 5 | 142 | 0.41 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1471 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1460 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 355 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 modified (disulfide, engineered).
Compared structures
- 5JEN · Crystal structure of the anti-sigma factor RsiV bound to lysozyme · the same entry in another collection · chain A against A, TM-score 1.00
- O05403 · AlphaFold monomer V2.0 prediction for anti-sigma-V factor rsiv (O05403) · a predicted model of the same protein · 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 O05403
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 5JEN · PDBe 5JEN · UniProt O05403 · UniProt P00698
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