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Crystal structure of lachnospiraceae bacterium ND2006 CPF1 in complex with crrna and target DNA (ttta pam)
Analyse Crystal structure of lachnospiraceae bacterium ND2006 CPF1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XUS
- Type
- protein + DNA + RNA
- Length
- 1,284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LBCPF1; Crrna; DNA (29-mer); DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*A)-3')
- Ligands
- NA, MG
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LBCPF1 | protein | 1206 | 48% helix, 14% strand | — |
| B | Crrna | rna | 40 | — | — |
| C | DNA (29-mer) | dna | 29 | — | — |
| D | DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.82 | 0.86 | 69 | EDO |
| 2 | 1010 | 0.76 | 0.78 | 53 | NA |
| 3 | 1140 | 0.75 | 0.78 | 73 | NA |
| 4 | 441 | 0.65 | 0.78 | 40 | empty |
| 5 | 92 | 0.58 | 0.87 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4086 Ų buried · 98 hydrogen bonds · protein-nucleic
- A–C · 2272 Ų buried · 44 hydrogen bonds · protein-nucleic
- B–C · 936 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- A–D · 626 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 403 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
- 5XUS · Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and… · 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
- Elsewhere: RCSB PDB 5XUS · PDBe 5XUS
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