MolNFT v1 · #154523 · protein + DNA
Crystal structure of TTCAS1-DNA complex
6KDV · CRISPR-associated endonuclease CAS1 2: “Crystal structure of TTCAS1-DNA complex”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #154523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KDV
- Type
- protein + DNA
- Length
- 1,144 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR-associated endonuclease CAS1 2; DNA (5'…
- EC
- 3.1.-.-
- UniProt
- Q53WG8
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | CRISPR-associated endonuclease CAS1 2 (EC 3.1.-.-) | protein | 283 | 45% helix, 14% strand | Q53WG8 |
| A | CRISPR-associated endonuclease CAS1 2 (EC 3.1.-.-) | protein | 263 | 50% helix, 17% strand | Q53WG8 |
| D | CRISPR-associated endonuclease CAS1 2 (EC 3.1.-.-) | protein | 280 | 47% helix, 15% strand | Q53WG8 |
| C | CRISPR-associated endonuclease CAS1 2 (EC 3.1.-.-) | protein | 264 | 49% helix, 18% strand | Q53WG8 |
| E, G | DNA (5'- D(*GP*AP*GP*TP*CP*GP*AP*TP*GP*CP*TP*GP*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP* T)-3') | dna | 15 | — | — |
| F | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP* C)-3') | dna | 11 | — | — |
| H | DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*CP*CP*AP*GP*CP*AP*TP*CP*GP*AP*CP*TP* C)-3') | dna | 13 | — | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.85 | 0.86 | 94 | empty |
| 2 | 150 | 0.80 | 0.97 | 27 | empty |
| 3 | 149 | 0.80 | 0.97 | 27 | empty |
| 4 | 189 | 0.71 | 0.88 | 33 | empty |
| 5 | 94 | 0.69 | 0.93 | 22 | empty |
Interfaces
19 interfaces between chains.
- B–A · 2633 Ų buried · 27 hydrogen bonds · protein-protein
- D–C · 2404 Ų buried · 27 hydrogen bonds · protein-protein
- A–G · 1185 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–E · 1102 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 734 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
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 Q53WG8
- Elsewhere: RCSB PDB 6KDV · PDBe 6KDV · UniProt Q53WG8
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