Research workbench
Crystal structure of methyltransferase ribozyme
Analyse Crystal structure of methyltransferase ribozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DLZ
- Type
- protein + RNA
- Length
- 468 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 small nuclear ribonucleoprotein a; RNA (45-mer)
- UniProt
- P09012
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U1 small nuclear ribonucleoprotein a | protein | 96 | 27% helix, 22% strand | P09012 |
| B | U1 small nuclear ribonucleoprotein a | protein | 87 | 29% helix, 24% strand | P09012 |
| C | U1 small nuclear ribonucleoprotein a | protein | 97 | 32% helix, 26% strand | P09012 |
| D | U1 small nuclear ribonucleoprotein a | protein | 98 | 30% helix, 27% strand | P09012 |
| X, Y | RNA (45-mer) | rna | 45 | — | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.71 | 0.76 | 71 | empty |
| 2 | 540 | 0.62 | 0.75 | 33 | empty |
| 3 | 254 | 0.52 | 0.75 | 34 | empty |
| 4 | 215 | 0.47 | 0.75 | 15 | empty |
| 5 | 111 | 0.47 | 0.80 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–X · 942 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–Y · 865 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 631 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 619 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 360 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7DLZ · Crystal Structure of Methyltransferase Ribozyme · 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 P09012
- Elsewhere: RCSB PDB 7DLZ · PDBe 7DLZ · UniProt P09012
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