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Crystal structure of yth domain of zygosaccharomyces rouxii MRB1 protein in complex with N6-methyladenosine RNA
Analyse Crystal structure of yth domain of zygosaccharomyces rouxii MRB1 protein in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U8T
- Type
- protein + RNA
- Length
- 971 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ZYRO0G01672P; RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3')
- UniProt
- C5E1V0
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ZYRO0G01672P | protein | 157 | 29% helix, 31% strand | C5E1V0 |
| B | ZYRO0G01672P | protein | 154 | 31% helix, 28% strand | C5E1V0 |
| C | ZYRO0G01672P | protein | 155 | 30% helix, 30% strand | C5E1V0 |
| D | ZYRO0G01672P | protein | 157 | 29% helix, 29% strand | C5E1V0 |
| E, F | ZYRO0G01672P | protein | 153 | 31% helix, 28% strand | C5E1V0 |
| O, P, Q, R, S, T | RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3') | rna | 7 | — | — |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.78 | 0.85 | 78 | empty |
| 2 | 489 | 0.76 | 0.85 | 79 | empty |
| 3 | 455 | 0.76 | 0.85 | 60 | empty |
| 4 | 315 | 0.67 | 0.83 | 30 | empty |
| 5 | 167 | 0.63 | 0.85 | 36 | empty |
Interfaces
32 interfaces between chains.
- A–O · 818 Ų buried · 21 hydrogen bonds · protein-nucleic
- F–R · 764 Ų buried · 24 hydrogen bonds · protein-nucleic
- E–S · 755 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–Q · 734 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–P · 733 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 modified (engineered, nucleotide modification).
Compared structures
- 4U8T · Crystal structure of YTH domain of Zygosaccharomyces rouxii MRB1 protein in complex with… · the same entry in another collection · chain A against A, 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 C5E1V0
- Elsewhere: RCSB PDB 4U8T · PDBe 4U8T · UniProt C5E1V0
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