Research workbench
1.80 ångström resolution crystal structure of a putative translation initiation inhibitor from vibrio vulnificus CMCP6
Analyse 1.80 ångström resolution crystal structure of a putative translation initiation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VCZ
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease L-psp
- UniProt
- Q8DCF8
- Ligands
- CA, MG
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Endoribonuclease L-psp | protein | 127 | 31% helix, 28% strand | Q8DCF8 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, C
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.83 | 0.97 | 31 | empty |
| 2 | 182 | 0.62 | 0.83 | 30 | GOL |
| 3 | 148 | 0.61 | 0.84 | 24 | GOL |
| 4 | 190 | 0.60 | 0.82 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–C · 919 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 917 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 907 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3VCZ · 1.80 Angstrom resolution crystal structure of a putative translation initiation inhibitor… · 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 Q8DCF8
- Elsewhere: RCSB PDB 3VCZ · PDBe 3VCZ · UniProt Q8DCF8
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