Research workbench
Minimal U1 snrnp
Analyse Minimal U1 snrnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJO
- Type
- protein + RNA
- Length
- 2,947 residues
- Chains
- 44
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small nuclear ribonucleoprotein sm D3; Small nuclear ribonucleoprotein-associated…
- UniProt
- P62318, P14678, P62314, P62316, P62304, P62306, P62308, P08621, P09234
- Ligands
- MG, K, ZN, CL, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 30 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small nuclear ribonucleoprotein sm D3 | protein | 84 | 19% helix, 46% strand | P62318 |
| B, P | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 83 | 8% helix, 53% strand | P14678 |
| C | Small nuclear ribonucleoprotein sm D1 | protein | 86 | 14% helix, 43% strand | P62314 |
| D | Small nuclear ribonucleoprotein sm D2 | protein | 98 | 19% helix, 46% strand | P62316 |
| E, e, S, s | Small nuclear ribonucleoprotein E | protein | 77 | 18% helix, 53% strand | P62304 |
| F | Small nuclear ribonucleoprotein F | protein | 73 | 15% helix, 58% strand | P62306 |
| G | Small nuclear ribonucleoprotein G | protein | 74 | 4% helix, 45% strand | P62308 |
| K, n | U1 small nuclear ribonucleoprotein 70 kda | protein | 58 | 28% helix, 0% strand | P08621 |
| L, l, M | U1 small nuclear ribonucleoprotein C | protein | 53 | 64% helix, 11% strand | P09234 |
| 1, 2 | U1 RNA variant (48-mer) with 4-helix junction replaced by kissing loop (HIV-1 (mal) dis) and shorter stem-loop 4. | rna | 48 | — | — |
| X, x, Y, y | RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3') | rna | 10 | — | — |
| a | Small nuclear ribonucleoprotein sm D3 | protein | 83 | 19% helix, 47% strand | P62318 |
| b | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 78 | 9% helix, 56% strand | P14678 |
| c | Small nuclear ribonucleoprotein sm D1 | protein | 87 | 16% helix, 38% strand | P62314 |
| d | Small nuclear ribonucleoprotein sm D2 | protein | 92 | 27% helix, 49% strand | P62316 |
| f, T, t | Small nuclear ribonucleoprotein F | protein | 74 | 15% helix, 57% strand | P62306 |
| g, u | Small nuclear ribonucleoprotein G | protein | 73 | 8% helix, 48% strand | P62308 |
| k | U1 small nuclear ribonucleoprotein 70 kda | protein | 57 | 23% helix, 0% strand | P08621 |
| O | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 20% helix, 48% strand | P62318 |
| Q | Small nuclear ribonucleoprotein sm D1 | protein | 85 | 14% helix, 44% strand | P62314 |
| R | Small nuclear ribonucleoprotein sm D2 | protein | 96 | 21% helix, 47% strand | P62316 |
| U | Small nuclear ribonucleoprotein G | protein | 71 | 0% helix, 49% strand | P62308 |
| N | U1 small nuclear ribonucleoprotein 70 kda | protein | 53 | 30% helix, 0% strand | P08621 |
| 3 | U1 RNA variant (48-mer) with 4-helix junction replaced by kissing loop (HIV-1 (mal) dis) and shorter stem-loop 4. | rna | 47 | — | — |
| o | Small nuclear ribonucleoprotein sm D3 | protein | 81 | 20% helix, 48% strand | P62318 |
| p | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 86 | 8% helix, 51% strand | P14678 |
| q | Small nuclear ribonucleoprotein sm D1 | protein | 87 | 14% helix, 43% strand | P62314 |
| r | Small nuclear ribonucleoprotein sm D2 | protein | 95 | 21% helix, 47% strand | P62316 |
| m | U1 small nuclear ribonucleoprotein C | protein | 50 | 62% helix, 12% strand | P09234 |
| 4 | U1 RNA variant (48-mer) with 4-helix junction replaced by kissing loop (HIV-1 (mal) dis) and shorter stem-loop 4. | rna | 49 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 20 copies · chains 1, B, l, 2, 3, 4, y, m
- K · Potassium ion · metal · 6 copies · chains 1, b, 2, Q, 3
- ZN · Zinc ion · metal · 4 copies · chains L, l, M, m
- CL · Chloride ion · ion · chains n, 4
- SO4 · Sulfate ion · ion · chains y
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains L, 1, l, 2
- EOH · Ethanol · additive · chains 4
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 | 587 | 0.86 | 0.92 | 74 | K, MG |
| 2 | 550 | 0.85 | 0.92 | 69 | MG |
| 3 | 1163 | 0.85 | 0.86 | 95 | MG |
| 4 | 733 | 0.85 | 0.89 | 80 | MG |
| 5 | 405 | 0.76 | 0.86 | 55 | empty |
Interfaces
129 interfaces between chains.
- C–D · 1229 Ų buried · 20 hydrogen bonds · protein-protein
- q–r · 1198 Ų buried · 20 hydrogen bonds · protein-protein
- c–d · 1164 Ų buried · 20 hydrogen bonds · protein-protein
- Q–R · 1154 Ų buried · 21 hydrogen bonds · protein-protein
- D–K · 1085 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4PJO · Minimal U1 snRNP · the same entry in another collection · chain L against L, 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 P62318
- Every structure of UniProt P14678
- Every structure of UniProt P62314
- Every structure of UniProt P62316
- Every structure of UniProt P62304
- Every structure of UniProt P62306
- Every structure of UniProt P62308
- Every structure of UniProt P08621
- Every structure of UniProt P09234
- Elsewhere: RCSB PDB 4PJO · PDBe 4PJO · UniProt P62318 · UniProt P14678 · UniProt P62314 · UniProt P62316 · UniProt P62304 · UniProt P62306 · UniProt P62308 · UniProt P08621 · UniProt P09234
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