Research workbench
Cryo-EM structure of the desulfovibrio vulgaris type I-C apo cascade
Analyse Cryo-EM structure of the desulfovibrio vulgaris type I-C apo cascade in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KHA
- Type
- protein + RNA
- Length
- 2,892 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated protein, CT1134 family; CRISPR-associated protein, TM1801 family…
- UniProt
- Q72WF9, Q72WF7, Q72WF8
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated protein, CT1134 family | protein | 220 | 10% helix, 26% strand | Q72WF9 |
| B, C, D, E, F, G, H | CRISPR-associated protein, TM1801 family | protein | 286 | 26% helix, 27% strand | Q72WF7 |
| I | CRISPR-associated protein, CT1133 family | protein | 385 | 37% helix, 7% strand | Q72WF8 |
| K, L | CRISPR-associated protein, CT1133 family | protein | 120 | 58% helix, 0% strand | Q72WF8 |
| J | RNA (45-mer) | rna | 45 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 771 | 0.87 | 0.90 | 121 | empty |
| 2 | 337 | 0.80 | 0.90 | 51 | empty |
| 3 | 127 | 0.77 | 0.96 | 29 | empty |
| 4 | 597 | 0.76 | 0.83 | 94 | empty |
| 5 | 578 | 0.76 | 0.83 | 72 | empty |
Interfaces
36 interfaces between chains.
- A–B · 2435 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 1728 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1721 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1711 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1691 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7KHA · Cryo-EM Structure of the Desulfovibrio vulgaris Type I-C Apo Cascade · 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 Q72WF9
- Every structure of UniProt Q72WF7
- Every structure of UniProt Q72WF8
- Elsewhere: RCSB PDB 7KHA · PDBe 7KHA · UniProt Q72WF9 · UniProt Q72WF7 · UniProt Q72WF8
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