MolNFT v1 · #190013 · protein + DNA + RNA
Plmcasx-SGRNAV1-dsdna ternary complex at nts loading state with flexible H2 domain
7WB0 · Ts-DNA: “Plmcasx-SGRNAV1-dsdna ternary complex at nts loading state with flexible H2 domain”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #190013 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7WB0
- Type
- protein + DNA + RNA
- Length
- 972 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ts-DNA; Nts-DNA; RNA (115-mer); Dplmcasx
- UniProt
- A0A1G3BXR9
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ts-DNA | dna | 33 | — | — |
| C | Nts-DNA | dna | 27 | — | — |
| D | RNA (115-mer) | rna | 115 | — | — |
| A | Dplmcasx | protein | 797 | 36% helix, 22% strand | A0A1G3BXR9 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.83 | 0.84 | 107 | empty |
| 2 | 1137 | 0.82 | 0.84 | 81 | empty |
| 3 | 969 | 0.76 | 0.79 | 78 | empty |
| 4 | 187 | 0.74 | 0.91 | 29 | empty |
| 5 | 362 | 0.64 | 0.79 | 33 | empty |
Interfaces
5 interfaces between chains.
- D–A · 3102 Ų buried · 45 hydrogen bonds · protein-nucleic
- C–A · 2083 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–A · 1550 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 939 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- B–C · 463 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7WB0 · PlmCasX-sgRNAv1-dsDNA ternary complex at nts loading state with flexible H2 domain · the same entry in another collection · chain B against B, 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 A0A1G3BXR9
- Elsewhere: RCSB PDB 7WB0 · PDBe 7WB0 · UniProt A0A1G3BXR9
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