Research workbench
Crystal structure of LSM2-8 complex, space group I212121
Analyse Crystal structure of LSM2-8 complex, space group I212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M77
- Type
- protein
- Length
- 1,054 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U6 snrna-associated sm-like protein LSM8; U6 snrna-associated sm-like protein LSM2; U6…
- UniProt
- P47093, P38203, P57743, Q06406, P40089, P53905, P40070
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 10 distinct chains · 13% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U6 snrna-associated sm-like protein LSM8 | protein | 83 | 8% helix, 48% strand | P47093 |
| B, I | U6 snrna-associated sm-like protein LSM2 | protein | 91 | 24% helix, 34% strand | P38203 |
| C | U6 snrna-associated sm-like protein LSM3 | protein | 69 | 13% helix, 59% strand | P57743 |
| D, K | U6 snrna-associated sm-like protein LSM6 | protein | 75 | 9% helix, 49% strand | Q06406 |
| E | U6 snrna-associated sm-like protein LSM5 | protein | 70 | 10% helix, 53% strand | P40089 |
| F, M | U6 snrna-associated sm-like protein LSM7 | protein | 65 | 6% helix, 55% strand | P53905 |
| G, N | U6 snrna-associated sm-like protein LSM4 | protein | 70 | 13% helix, 51% strand | P40070 |
| H | U6 snrna-associated sm-like protein LSM8 | protein | 85 | 18% helix, 45% strand | P47093 |
| J | U6 snrna-associated sm-like protein LSM3 | protein | 72 | 13% helix, 57% strand | P57743 |
| L | U6 snrna-associated sm-like protein LSM5 | protein | 73 | 14% helix, 56% strand | P40089 |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.72 | 0.81 | 50 | empty |
| 2 | 70 | 0.71 | 0.96 | 21 | empty |
| 3 | 123 | 0.60 | 0.85 | 32 | empty |
| 4 | 177 | 0.49 | 0.77 | 23 | empty |
| 5 | 106 | 0.43 | 0.77 | 17 | empty |
Interfaces
21 interfaces between chains.
- I–J · 1306 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1285 Ų buried · 21 hydrogen bonds · protein-protein
- L–M · 941 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 937 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 914 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4M77 · Crystal structure of Lsm2-8 complex, space group I212121 · the same entry in another collection · chain N against N, 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 P47093
- Every structure of UniProt P38203
- Every structure of UniProt P57743
- Every structure of UniProt Q06406
- Every structure of UniProt P40089
- Every structure of UniProt P53905
- Every structure of UniProt P40070
- Elsewhere: RCSB PDB 4M77 · PDBe 4M77 · UniProt P47093 · UniProt P38203 · UniProt P57743 · UniProt Q06406 · UniProt P40089 · UniProt P53905 · UniProt P40070
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