MolNFT v1 · #139939 · protein + DNA + RNA
Crystal structure of lachnospiraceae bacterium ND2006 CPF1 in complex with crrna and target DNA (ccca pam)
5XUZ · LBCPF1: “Crystal structure of lachnospiraceae bacterium ND2006 CPF1 in complex with crrna and target DNA (ccca pam)”. X-ray diffraction, 2 ligands (NA, MG), 20 pockets (best druggability 0.83). MolNFT v1 #139939 on GenesisL1: 3D…
- 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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