Research workbench
Structure of S. pombe LSM1-7 with RNA, polyuridine with 3' guanosine
Analyse Structure of S. pombe LSM1-7 with RNA, polyuridine with 3' guanosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PPV
- Type
- protein + RNA
- Length
- 556 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U6 snrna-associated sm-like protein LSM1; U6 snrna-associated sm-like protein LSM2…
- UniProt
- P87173, O94408, Q9Y7M4, O14352, O42978, Q9UUI1, O74499
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 8 distinct chains · 17% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U6 snrna-associated sm-like protein LSM1 | protein | 69 | 10% helix, 65% strand | P87173 |
| B | U6 snrna-associated sm-like protein LSM2 | protein | 93 | 37% helix, 34% strand | O94408 |
| C | Probable U6 snrna-associated sm-like protein LSM3 | protein | 75 | 11% helix, 60% strand | Q9Y7M4 |
| D | Probable U6 snrna-associated sm-like protein LSM4 | protein | 82 | 22% helix, 48% strand | O14352 |
| E | U6 snrna-associated sm-like protein LSM5 | protein | 75 | 13% helix, 55% strand | O42978 |
| F | U6 snrna-associated sm-like protein LSM6 | protein | 71 | 17% helix, 59% strand | Q9UUI1 |
| G | U6 snrna-associated sm-like protein LSM7 | protein | 85 | 5% helix, 56% strand | O74499 |
| H | RNA (5'-R(*AP*UP*UP*UP*UP*G)-3') | rna | 6 | — | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.72 | 0.78 | 88 | empty |
| 2 | 145 | 0.46 | 0.76 | 23 | empty |
| 3 | 89 | 0.39 | 0.77 | 22 | empty |
| 4 | 55 | 0.31 | 0.76 | 13 | empty |
Interfaces
14 interfaces between chains.
- B–C · 1032 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 967 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 953 Ų buried · 19 hydrogen bonds · protein-protein
- E–G · 927 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 788 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6PPV · Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' guanosine · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y7M4 · AlphaFold monomer V2.0 prediction for probable U6 snrna-associated sm-like protein LSM3… · a predicted model of the same protein · chain C against A, TM-score 0.98
- O42978 · AlphaFold monomer V2.0 prediction for U6 snrna-associated sm-like protein LSM5 (O42978) · a predicted model of the same protein · chain E against A, TM-score 0.97
- O14352 · AlphaFold monomer V2.0 prediction for probable U6 snrna-associated sm-like protein LSM4… · a predicted model of the same protein · chain D against A, TM-score 0.96
- P87173 · AlphaFold monomer V2.0 prediction for U6 snrna-associated sm-like protein LSM1 (P87173) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P87173
- Every structure of UniProt O94408
- Every structure of UniProt Q9Y7M4
- Every structure of UniProt O14352
- Every structure of UniProt O42978
- Every structure of UniProt Q9UUI1
- Every structure of UniProt O74499
- Elsewhere: RCSB PDB 6PPV · PDBe 6PPV · UniProt P87173 · UniProt O94408 · UniProt Q9Y7M4 · UniProt O14352 · UniProt O42978 · UniProt Q9UUI1 · UniProt O74499
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