MolNFT v1 · #88088 · protein
Vaccinia virus capping enzyme complexed with GTP and sah
4CKB · MRNA-capping enzyme catalytic subunit: “Vaccinia virus capping enzyme complexed with GTP and sah”. X-ray diffraction, 2 ligands (SAH, GTP), 20 pockets (best druggability 0.84). MolNFT v1 #88088 on GenesisL1: 3D structure, binding…
- PDB
- 4CKB
- Type
- protein
- Length
- 2,191 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-capping enzyme catalytic subunit; MRNA-capping enzyme regulatory subunit
- EC
- 3.1.3.33, 2.7.7.50, 2.1.1.56
- UniProt
- P04298, P04318
- Ligands
- SAH, GTP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-capping enzyme catalytic subunit (EC 3.1.3.33, 2.7.7.50, 2.1.1.56) | protein | 809 | 29% helix, 35% strand | P04298 |
| B, E | MRNA-capping enzyme regulatory subunit | protein | 284 | 43% helix, 16% strand | P04318 |
| D | MRNA-capping enzyme catalytic subunit (EC 3.1.3.33, 2.7.7.50, 2.1.1.56) | protein | 814 | 29% helix, 35% strand | P04298 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D
- GTP · Guanosine-5'-triphosphate · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.84 | 0.84 | 100 | GTP |
| 2 | 1179 | 0.82 | 0.82 | 105 | empty |
| 3 | 1131 | 0.79 | 0.81 | 84 | SAH |
| 4 | 1184 | 0.78 | 0.80 | 92 | SAH |
| 5 | 280 | 0.74 | 0.87 | 38 | empty |
Interfaces
3 interfaces between chains.
- D–E · 1612 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1592 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 133 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4CKB · Vaccinia virus capping enzyme complexed with GTP and SAH · the same entry in another collection · chain B against B, 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 P04298
- Every structure of UniProt P04318
- Elsewhere: RCSB PDB 4CKB · PDBe 4CKB · UniProt P04298 · UniProt P04318
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