Research workbench
Cryo-EM structure of yeast ribonuclease mrp with substrate ITS1
Analyse Cryo-EM structure of yeast ribonuclease mrp with substrate ITS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C7A
- Type
- protein + RNA
- Length
- 2,858 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease mrp RNA subunit NME1; Ribonucleases P/MRP protein subunit POP1…
- EC
- 3.1.26.5
- UniProt
- P41812, P53833, P38336, P28005, P53218, P38291, P38208, P38786, P40993, Q12530
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 13 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease mrp RNA subunit NME1 | rna | 330 | — | — |
| B | Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5) | protein | 793 | 35% helix, 17% strand | P41812 |
| C | Ribonucleases P/MRP protein subunit POP3 | protein | 152 | 34% helix, 14% strand | P53833 |
| D | Rnases MRP/P 32.9 kda subunit | protein | 251 | 45% helix, 17% strand | P38336 |
| E | Ribonuclease P/MRP protein subunit POP5 (EC 3.1.26.5) | protein | 145 | 41% helix, 21% strand | P28005 |
| F | Ribonucleases P/MRP protein subunit POP6 (EC 3.1.26.5) | protein | 157 | 25% helix, 34% strand | P53218 |
| G | Ribonucleases P/MRP protein subunit POP7 (EC 3.1.26.5) | protein | 121 | 28% helix, 35% strand | P38291 |
| H | Ribonucleases P/MRP protein subunit POP8 (EC 3.1.26.5) | protein | 131 | 41% helix, 21% strand | P38208 |
| I | Ribonuclease P/MRP protein subunit RPP1 (EC 3.1.26.5) | protein | 242 | 43% helix, 18% strand | P38786 |
| J | Ribonuclease P/MRP protein subunit RPP1 (EC 3.1.26.5) | protein | 292 | 37% helix, 15% strand | P38786 |
| K | Ribonuclease mrp protein subunit SNM1 | protein | 104 | 42% helix, 11% strand | P40993 |
| L | Ribonuclease mrp protein subunit RMP1 | protein | 131 | 78% helix, 0% strand | Q12530 |
| R | Internal transcribed spacer 1 | rna | 9 | — | — |
Ligands and binding sites
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 | 961 | 0.84 | 0.86 | 77 | MG |
| 2 | 796 | 0.82 | 0.86 | 60 | empty |
| 3 | 328 | 0.82 | 0.92 | 42 | empty |
| 4 | 432 | 0.82 | 0.91 | 62 | empty |
| 5 | 1143 | 0.82 | 0.83 | 79 | empty |
Interfaces
33 interfaces between chains.
- A–B · 8213 Ų buried · 142 hydrogen bonds · protein-nucleic
- D–J · 2402 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 2042 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–L · 1927 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1873 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 7C7A · Cryo-EM structure of yeast Ribonuclease MRP with substrate ITS1 · the same entry in another collection · chain R against R, 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 P41812
- Every structure of UniProt P53833
- Every structure of UniProt P38336
- Every structure of UniProt P28005
- Every structure of UniProt P53218
- Every structure of UniProt P38291
- Every structure of UniProt P38208
- Every structure of UniProt P38786
- Every structure of UniProt P40993
- Every structure of UniProt Q12530
- Elsewhere: RCSB PDB 7C7A · PDBe 7C7A · UniProt P41812 · UniProt P53833 · UniProt P38336 · UniProt P28005 · UniProt P53218 · UniProt P38291 · UniProt P38208 · UniProt P38786 · UniProt P40993 · UniProt Q12530
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