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Crystal structure of lachnospiraceae bacterium ND2006 CPF1 in complex with crrna and target DNA (ccca 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
- 5XUZ
- Type
- protein + DNA + RNA
- Length
- 2,580 residues
- Chains
- 8
- 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*CP*CP*CP*A)-3')
- Ligands
- NA, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LBCPF1 | protein | 1216 | 48% helix, 14% strand | — |
| B, F | Crrna | rna | 40 | — | — |
| C, G | DNA (29-mer) | dna | 29 | — | — |
| D, H | DNA (5'-D(*CP*GP*TP*CP*CP*CP*CP*CP*A)-3') | dna | 9 | — | — |
| E | LBCPF1 | protein | 1208 | 48% helix, 14% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains B, C, F, G
- MG · Magnesium ion · metal · 2 copies · chains A, B, E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, E, F, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.83 | 0.86 | 87 | empty |
| 2 | 606 | 0.82 | 0.88 | 68 | empty |
| 3 | 1013 | 0.81 | 0.83 | 74 | empty |
| 4 | 967 | 0.80 | 0.82 | 88 | empty |
| 5 | 624 | 0.79 | 0.84 | 43 | EDO |
Interfaces
12 interfaces between chains.
- E–F · 4076 Ų buried · 94 hydrogen bonds · protein-nucleic
- A–B · 4075 Ų buried · 103 hydrogen bonds · protein-nucleic
- E–G · 2341 Ų buried · 41 hydrogen bonds · protein-nucleic
- A–C · 2296 Ų buried · 43 hydrogen bonds · protein-nucleic
- A–E · 1322 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5XUZ · 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 5XUZ · PDBe 5XUZ
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