Research workbench
Structure of acinetobacter baumannii CAP4 SAVED/CARF-domain containing receptor with the cyclic trinucleotide 3'3'3'-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
- 6WAN
- Type
- protein + RNA
- Length
- 2,619 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saved domain-containing protein; Cyclic RNA (R(P*AP*AP*A)
- UniProt
- C0VHC9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Saved domain-containing protein | protein | 438 | 43% helix, 21% strand | C0VHC9 |
| D | Saved domain-containing protein | protein | 435 | 45% helix, 21% strand | C0VHC9 |
| E | Saved domain-containing protein | protein | 437 | 44% helix, 21% strand | C0VHC9 |
| F | Saved domain-containing protein | protein | 415 | 44% helix, 20% strand | C0VHC9 |
| G, H, I, J, K, L | Cyclic RNA (R(P*AP*AP*A) | rna | 3 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.87 | 0.88 | 138 | empty |
| 2 | 742 | 0.86 | 0.89 | 84 | empty |
| 3 | 827 | 0.81 | 0.84 | 85 | empty |
| 4 | 814 | 0.81 | 0.84 | 86 | empty |
| 5 | 352 | 0.77 | 0.87 | 54 | empty |
Interfaces
18 interfaces between chains.
- A–C · 960 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 955 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 902 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 893 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 867 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6WAN · Structure of Acinetobacter baumannii Cap4 SAVED/CARF-domain containing receptor with the… · the same entry in another collection · chain L against L, 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 C0VHC9
- Elsewhere: RCSB PDB 6WAN · PDBe 6WAN · UniProt C0VHC9
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