MolNFT v1 · #139965 · protein + DNA
E. fae CAS1-CAS2/PRESPACER/TARGET ternary complex revealing the fully integrated states
5XVP · CRISPR-associated endonuclease CAS1: “E. fae CAS1-CAS2/PRESPACER/TARGET ternary complex revealing the fully integrated states”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.83). MolNFT v1 #139965 on GenesisL1…
- PDB
- 5XVP
- Type
- protein + DNA
- Length
- 1,515 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS1; CRISPR-associated endoribonuclease CAS2; DNA…
- EC
- 3.1.-.-
- UniProt
- E6GPD7, E6GPD6
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 286 | 50% helix, 17% strand | E6GPD7 |
| B, C, D | CRISPR-associated endonuclease CAS1 (EC 3.1.-.-) | protein | 288 | 50% helix, 17% strand | E6GPD7 |
| E | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 104 | 37% helix, 33% strand | E6GPD6 |
| F | CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-) | protein | 102 | 37% helix, 31% strand | E6GPD6 |
| G | DNA (73-mer) | dna | 71 | — | — |
| H | DNA (73-mer) | dna | 71 | — | — |
| I | DNA (5'-D(P*TP*TP*CP*TP*CP*CP*GP*AP*G)-3') | dna | 9 | — | — |
| J | DNA (5'-D(P*TP*TP*CP*TP*CP*CP*GP*AP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains E, F, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.83 | 0.84 | 104 | empty |
| 2 | 692 | 0.79 | 0.84 | 55 | empty |
| 3 | 580 | 0.72 | 0.80 | 62 | empty |
| 4 | 685 | 0.71 | 0.78 | 57 | empty |
| 5 | 548 | 0.71 | 0.80 | 43 | empty |
Interfaces
24 interfaces between chains.
- G–H · 2629 Ų buried · 251 hydrogen bonds · nucleic-nucleic
- C–D · 2074 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2061 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1434 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 1091 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5XVP · E. fae Cas1-Cas2/prespacer/target ternary complex revealing the fully integrated states · 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 E6GPD7
- Every structure of UniProt E6GPD6
- Elsewhere: RCSB PDB 5XVP · PDBe 5XVP · UniProt E6GPD7 · UniProt E6GPD6
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