MolNFT v1 · #152455 · protein
Crystal structure of the makes caterpillars floppy (mcf)-like effector of vibrio vulnificus MO6-24/O in complex with a human ADP- ribosylation factor 3 (ARF3)
6II6 · Putative rtx-toxin: “Crystal structure of the makes caterpillars floppy (mcf)-like effector of vibrio vulnificus MO6-24/O in…”. X-ray diffraction, 2 ligands (GTP, MG), 16 pockets (best druggability 0.81). MolNFT v1 #152455 on…
- PDB
- 6II6
- Type
- protein
- Length
- 1,017 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative rtx-toxin; ADP-ribosylation factor 3
- UniProt
- P61204
- Ligands
- GTP, MG
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative rtx-toxin | protein | 349 | 53% helix, 13% strand | — |
| B | Putative rtx-toxin | protein | 340 | 52% helix, 13% strand | — |
| C | ADP-ribosylation factor 3 | protein | 164 | 35% helix, 27% strand | P61204 |
| D | ADP-ribosylation factor 3 | protein | 164 | 31% helix, 27% strand | P61204 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.81 | 0.82 | 121 | empty |
| 2 | 663 | 0.76 | 0.81 | 45 | empty |
| 3 | 285 | 0.68 | 0.83 | 35 | empty |
| 4 | 590 | 0.66 | 0.76 | 53 | empty |
| 5 | 263 | 0.62 | 0.80 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1240 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1209 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 466 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 6II6 · Crystal structure of the Makes Caterpillars Floppy (MCF)-Like effector of Vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- P61204 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 3 (P61204) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P61204
- Elsewhere: RCSB PDB 6II6 · PDBe 6II6 · UniProt P61204
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