Research workbench
Crystal structure of the SRP54-SRP19-7S.S srp RNA complex of M. jannaschii
Analyse Crystal structure of the SRP54-SRP19-7S.S srp RNA complex of M. jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V3C
- Type
- protein + RNA
- Length
- 1,170 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 19 kda protein; Signal recognition 54 kda protein; 7S RNA
- UniProt
- Q58440, Q57565
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Signal recognition particle 19 kda protein | protein | 87 | 34% helix, 14% strand | Q58440 |
| C | Signal recognition 54 kda protein | protein | 403 | 45% helix, 8% strand | Q57565 |
| D | Signal recognition 54 kda protein | protein | 401 | 35% helix, 5% strand | Q57565 |
| M, N | 7S RNA | rna | 96 | — | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.80 | 0.84 | 60 | empty |
| 2 | 1146 | 0.79 | 0.81 | 101 | empty |
| 3 | 771 | 0.78 | 0.83 | 71 | empty |
| 4 | 768 | 0.78 | 0.82 | 66 | empty |
| 5 | 87 | 0.76 | 0.97 | 22 | empty |
Interfaces
9 interfaces between chains.
- C–M · 1508 Ų buried · 36 hydrogen bonds · protein-nucleic
- B–N · 1188 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–M · 1182 Ų buried · 31 hydrogen bonds · protein-nucleic
- D–N · 898 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 207 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2V3C · Crystal structure of the SRP54-SRP19-7S.S SRP RNA complex of M. jannaschii · the same entry in another collection · chain N against N, TM-score 1.00
- Q58440 · AlphaFold monomer V2.0 prediction for signal recognition particle 19 kda protein (Q58440) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q57565 · AlphaFold monomer V2.0 prediction for signal recognition particle 54 kda protein (Q57565) · a predicted model of the same protein · chain C against A, TM-score 0.68
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 Q58440
- Every structure of UniProt Q57565
- Elsewhere: RCSB PDB 2V3C · PDBe 2V3C · UniProt Q58440 · UniProt Q57565
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