MolNFT v1 · #154448 · protein
Fused to-MTBCSM1 with 2DATP
6KBD · CRISPR system single-strand-specific deoxyribonuclease…: “Fused to-MTBCSM1 with 2DATP”. X-ray diffraction, 2 ligands (DTP, MG), 10 pockets (best druggability 0.82). MolNFT v1 #154448 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KBD
- Type
- protein
- Length
- 616 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-A),CRISPR…
- EC
- 3.1.-.-, 2.7.7.-
- UniProt
- B6YWB8, P71629
- Ligands
- DTP, MG
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-A),CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a) (EC 3.1.-.-, 2.7.7.-) | protein | 616 | 49% helix, 16% strand | B6YWB8, P71629 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.82 | 0.85 | 67 | DTP, MG |
| 2 | 100 | 0.76 | 0.96 | 20 | empty |
| 3 | 76 | 0.63 | 0.91 | 23 | empty |
| 4 | 127 | 0.56 | 0.83 | 20 | empty |
| 5 | 73 | 0.55 | 0.87 | 24 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6KBD · fused To-MtbCsm1 with 2dATP · the same entry in another collection · chain A against A, TM-score 1.00
- B6YWB8 · AlphaFold monomer V2.0 prediction for CRISPR system single-strand- specific… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P71629 · AlphaFold monomer V2.0 prediction for CRISPR system single-strand- specific… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 B6YWB8
- Every structure of UniProt P71629
- Elsewhere: RCSB PDB 6KBD · PDBe 6KBD · UniProt B6YWB8 · UniProt P71629
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