Research workbench
Structure of acinetobacter baumannii CAP4 SAVED/CARF-domain containing receptor with the cyclic trinucleotide 2'3'3'-caaa
Analyse Structure of acinetobacter baumannii CAP4 SAVED/CARF-domain containing receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VM6
- Type
- protein + RNA
- Length
- 2,641 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saved domain-containing protein; 2'-5'-linked cyclic RNA (5'-R(P*AP*AP*A)-3')
- UniProt
- C0VHC9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Saved domain-containing protein | protein | 438 | 45% helix, 21% strand | C0VHC9 |
| B, D | Saved domain-containing protein | protein | 440 | 45% helix, 21% strand | C0VHC9 |
| C | Saved domain-containing protein | protein | 439 | 44% helix, 21% strand | C0VHC9 |
| E | Saved domain-containing protein | protein | 432 | 45% helix, 21% strand | C0VHC9 |
| F | Saved domain-containing protein | protein | 437 | 45% helix, 21% strand | C0VHC9 |
| G, H, I, J, K | 2'-5'-linked cyclic RNA (5'-R(P*AP*AP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.86 | 0.87 | 145 | SO4 |
| 2 | 1108 | 0.86 | 0.87 | 134 | SO4 |
| 3 | 945 | 0.82 | 0.83 | 92 | empty |
| 4 | 586 | 0.79 | 0.85 | 67 | empty |
| 5 | 500 | 0.76 | 0.84 | 54 | empty |
Interfaces
17 interfaces between chains.
- C–D · 920 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 910 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 902 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 884 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 883 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6VM6 · Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor with the… · the same entry in another collection · chain K against K, TM-score 1.00
- C0VHC9 · AlphaFold monomer V2.0 prediction for CD-ntase-associated protein 4 (C0VHC9) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 C0VHC9
- Elsewhere: RCSB PDB 6VM6 · PDBe 6VM6 · UniProt C0VHC9
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