MolNFT v1 · #78206 · protein
Crystal structure of human mRNA guanylyltransferase
3S24 · MRNA-capping enzyme: “Crystal structure of human mRNA guanylyltransferase”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.81). MolNFT v1 #78206 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3S24
- Type
- protein
- Length
- 2,277 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-capping enzyme
- EC
- 3.1.3.33, 2.7.7.50
- UniProt
- O60942
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MRNA-capping enzyme (EC 3.1.3.33, 2.7.7.50) | protein | 328 | 23% helix, 37% strand | O60942 |
| B | MRNA-capping enzyme (EC 3.1.3.33, 2.7.7.50) | protein | 316 | 23% helix, 34% strand | O60942 |
| C | MRNA-capping enzyme (EC 3.1.3.33, 2.7.7.50) | protein | 314 | 24% helix, 35% strand | O60942 |
| E | MRNA-capping enzyme (EC 3.1.3.33, 2.7.7.50) | protein | 329 | 24% helix, 32% strand | O60942 |
| G | MRNA-capping enzyme (EC 3.1.3.33, 2.7.7.50) | protein | 329 | 20% helix, 32% strand | O60942 |
| F | MRNA-capping enzyme (EC 3.1.3.33, 2.7.7.50) | protein | 333 | 26% helix, 31% strand | O60942 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1000 | 0.81 | 0.82 | 107 | empty |
| 2 | 1146 | 0.77 | 0.79 | 106 | empty |
| 3 | 927 | 0.75 | 0.78 | 69 | SO4 |
| 4 | 750 | 0.75 | 0.80 | 74 | empty |
| 5 | 755 | 0.75 | 0.80 | 71 | empty |
Interfaces
11 interfaces between chains.
- C–F · 1052 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 943 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 937 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 930 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 772 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 O60942
- Elsewhere: RCSB PDB 3S24 · PDBe 3S24 · UniProt O60942
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