Research workbench
Structure of the V. cholerae rtx cysteine protease domain in complex with an aza-leucine peptide inhibitor
Analyse Structure of the V. cholerae rtx cysteine protease domain in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GCD
- Type
- protein
- Length
- 808 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rtx toxin rtxa
- UniProt
- Q9KS12
- Ligands
- AZ0, IHP, NA
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Rtx toxin rtxa | protein | 202 | 27% helix, 26% strand | Q9KS12 |
Ligands and binding sites
- AZ0 · ethyl (5S,8S,14S)-14-hydroxy-5,8,11-tris(2-methylpropyl)-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate · ligand · 4 copies · chains A, B, C, D
- IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, 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 | 717 | 0.75 | 0.80 | 57 | IHP, NA |
| 2 | 574 | 0.68 | 0.78 | 56 | empty |
| 3 | 208 | 0.56 | 0.79 | 27 | IHP |
| 4 | 182 | 0.55 | 0.80 | 27 | IHP |
| 5 | 185 | 0.53 | 0.79 | 27 | IHP |
Interfaces
5 interfaces between chains.
- A–B · 429 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 261 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 229 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3GCD · Structure of the V. cholerae RTX cysteine protease domain in complex with an aza-Leucine… · 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 Q9KS12
- Elsewhere: RCSB PDB 3GCD · PDBe 3GCD · UniProt Q9KS12
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