MolNFT v1 · #158455 · protein + RNA
Small conformation of ssrna-bound CRISPR_CSM complex
6NUD · CRISPR system cms protein CSM2: “Small conformation of ssrna-bound CRISPR_CSM complex”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.90). MolNFT v1 #158455 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NUD
- Type
- protein + RNA
- Length
- 2,488 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CRISPR system cms protein CSM2; Crrna; CRISPR type III-associated ramp protein CSM4…
- EC
- 3.1.-.-, 2.7.7.-
- UniProt
- A0A0A7HIX1, A0A0A7HGA1, A0A0A7HFE1, A0A0A7HIF0
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 6 distinct chains · 29% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, M | CRISPR system cms protein CSM2 | protein | 108 | 54% helix, 0% strand | A0A0A7HIX1 |
| H | Crrna | rna | 40 | — | — |
| I | CRISPR type III-associated ramp protein CSM4 | protein | 295 | 16% helix, 14% strand | A0A0A7HGA1 |
| J | CRISPR system single-strand-specific deoxyribonuclease CAS10/CSM1 (subtype III-a) (EC 3.1.-.-, 2.7.7.-) | protein | 741 | 34% helix, 8% strand | A0A0A7HFE1 |
| U | Target ssrna | rna | 28 | — | — |
| C, E, N, O, P | CRISPR type III-associated ramp protein CSM3 | protein | 212 | 14% helix, 21% strand | A0A0A7HIF0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains I, J
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 | 917 | 0.90 | 0.93 | 113 | empty |
| 2 | 1147 | 0.89 | 0.91 | 135 | empty |
| 3 | 1054 | 0.88 | 0.90 | 103 | empty |
| 4 | 662 | 0.86 | 0.91 | 83 | empty |
| 5 | 774 | 0.82 | 0.85 | 81 | ATP |
Interfaces
45 interfaces between chains.
- I–J · 1976 Ų buried · 21 hydrogen bonds · protein-protein
- C–P · 1741 Ų buried · 15 hydrogen bonds · protein-protein
- E–P · 1637 Ų buried · 16 hydrogen bonds · protein-protein
- E–O · 1632 Ų buried · 16 hydrogen bonds · protein-protein
- N–O · 1566 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6NUD · Small conformation of ssRNA-bound CRISPR_Csm complex · the same entry in another collection · chain U against U, 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
- Every structure of UniProt A0A0A7HIX1
- Every structure of UniProt A0A0A7HGA1
- Every structure of UniProt A0A0A7HFE1
- Every structure of UniProt A0A0A7HIF0
- Elsewhere: RCSB PDB 6NUD · PDBe 6NUD · UniProt A0A0A7HIX1 · UniProt A0A0A7HGA1 · UniProt A0A0A7HFE1 · UniProt A0A0A7HIF0
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