Research workbench
Human 17S U2 snrnp
Analyse Human 17S U2 snrnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y5Q
- Type
- protein + RNA
- Length
- 4,911 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger-like domain-containing protein 5A; Splicing factor 3B subunit 5; Splicing…
- EC
- 3.6.4.13
- UniProt
- Q7RTV0, Q9BWJ5, Q13435, Q15393, O75533, Q7L014, P09661, P08579, Q9Y3B4, Q15459, Q15428, Q12874, Q15427, P14678, P62308, P62314, P62316, P62318, P62304, P62306, O43719
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 22 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| y | Phd finger-like domain-containing protein 5A | protein | 93 | 11% helix, 16% strand | Q7RTV0 |
| x | Splicing factor 3B subunit 5 | protein | 66 | 53% helix, 0% strand | Q9BWJ5 |
| 8 | Splicing factor 3B subunit 2 | protein | 172 | 24% helix, 5% strand | Q13435 |
| v | Splicing factor 3B subunit 3 | protein | 1177 | 7% helix, 39% strand | Q15393 |
| u | Splicing factor 3B subunit 1 | protein | 863 | 69% helix, 0% strand | O75533 |
| p | Probable ATP-dependent RNA helicase DDX46 (EC 3.6.4.13) | protein | 445 | 42% helix, 13% strand | Q7L014 |
| a | U2 small nuclear ribonucleoprotein a' | protein | 162 | 23% helix, 17% strand | P09661 |
| b | U2 small nuclear ribonucleoprotein B'' | protein | 166 | 28% helix, 27% strand | P08579 |
| z | Splicing factor 3B subunit 6 | protein | 77 | 23% helix, 22% strand | Q9Y3B4 |
| 6 | Splicing factor 3A subunit 1 | protein | 123 | 59% helix, 0% strand | Q15459 |
| 7 | Splicing factor 3A subunit 2 | protein | 100 | 4% helix, 33% strand | Q15428 |
| 9 | Splicing factor 3A subunit 3 | protein | 420 | 53% helix, 3% strand | Q12874 |
| o | Splicing factor 3B subunit 4 | protein | 160 | 23% helix, 29% strand | Q15427 |
| m | Small nuclear ribonucleoprotein-associated proteins B and B' | protein | 71 | 4% helix, 52% strand | P14678 |
| k | Small nuclear ribonucleoprotein G | protein | 74 | 0% helix, 50% strand | P62308 |
| n | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 12% helix, 46% strand | P62314 |
| h | Small nuclear ribonucleoprotein sm D2 | protein | 98 | 16% helix, 45% strand | P62316 |
| l | Small nuclear ribonucleoprotein sm D3 | protein | 83 | 10% helix, 43% strand | P62318 |
| j | Small nuclear ribonucleoprotein E | protein | 79 | 14% helix, 53% strand | P62304 |
| i | Small nuclear ribonucleoprotein F | protein | 74 | 9% helix, 58% strand | P62306 |
| q | HIV tat-specific factor 1 | protein | 178 | 25% helix, 23% strand | O43719 |
| 2 | U2SNRNA | rna | 148 | — | — |
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 | 939 | 0.75 | 0.79 | 120 | empty |
| 2 | 916 | 0.75 | 0.79 | 97 | empty |
| 3 | 848 | 0.74 | 0.79 | 119 | empty |
| 4 | 818 | 0.72 | 0.78 | 90 | empty |
| 5 | 685 | 0.72 | 0.80 | 98 | empty |
Interfaces
40 interfaces between chains.
- h–2 · 634 Ų buried · 18 hydrogen bonds · protein-nucleic
- 8–u · 546 Ų buried · 1 hydrogen bond · protein-protein
- b–2 · 472 Ų buried · 10 hydrogen bonds · protein-nucleic
- v–u · 376 Ų buried · 1 hydrogen bond · protein-protein
- l–2 · 371 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6Y5Q · human 17S U2 snRNP · the same entry in another collection · chain 7 against 7, 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 Q7RTV0
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt Q13435
- Every structure of UniProt Q15393
- Every structure of UniProt O75533
- Every structure of UniProt Q7L014
- Every structure of UniProt P09661
- Every structure of UniProt P08579
- Every structure of UniProt Q9Y3B4
- Every structure of UniProt Q15459
- Every structure of UniProt Q15428
- Every structure of UniProt Q12874
- Every structure of UniProt Q15427
- Every structure of UniProt P14678
- Every structure of UniProt P62308
- Every structure of UniProt P62314
- Every structure of UniProt P62316
- Every structure of UniProt P62318
- Every structure of UniProt P62304
- Every structure of UniProt P62306
- Every structure of UniProt O43719
- Elsewhere: RCSB PDB 6Y5Q · PDBe 6Y5Q · UniProt Q7RTV0 · UniProt Q9BWJ5 · UniProt Q13435 · UniProt Q15393 · UniProt O75533 · UniProt Q7L014 · UniProt P09661 · UniProt P08579 · UniProt Q9Y3B4 · UniProt Q15459 · UniProt Q15428 · UniProt Q12874 · UniProt Q15427 · UniProt P14678 · UniProt P62308 · UniProt P62314 · UniProt P62316 · UniProt P62318 · UniProt P62304 · UniProt P62306 · UniProt O43719
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