MolNFT v1 · #137859 · protein + RNA
Crystal structure of LBACAS13A (C2C2) bound to mature crrna (20-nt spacer)
5W1I: “Crystal structure of LBACAS13A (C2C2) bound to mature crrna (20-nt spacer)”. X-ray diffraction, 1 ligand (IOD), 20 pockets (best druggability 0.89). MolNFT v1 #137859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W1I
- Type
- protein + RNA
- Length
- 2,668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mature crrna; LBACAS13A (C2C2)
- Ligands
- IOD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mature crrna | rna | 39 | — | — |
| A | LBACAS13A (C2C2) | protein | 1294 | 57% helix, 8% strand | — |
| D | Mature crrna | rna | 37 | — | — |
| C | LBACAS13A (C2C2) | protein | 1298 | 57% helix, 8% strand | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 16 copies · chains A, C
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 | 1035 | 0.89 | 0.91 | 97 | empty |
| 2 | 1183 | 0.87 | 0.88 | 114 | empty |
| 3 | 1047 | 0.84 | 0.85 | 97 | empty |
| 4 | 188 | 0.83 | 0.97 | 24 | empty |
| 5 | 1083 | 0.83 | 0.84 | 106 | empty |
Interfaces
3 interfaces between chains.
- B–A · 5382 Ų buried · 121 hydrogen bonds · protein-nucleic
- D–C · 4987 Ų buried · 107 hydrogen bonds · protein-nucleic
- A–C · 645 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5W1I · Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (20-nt spacer) · the same entry in another collection · chain B against B, 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 5W1I · PDBe 5W1I
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