MolNFT v1 · #88089 · protein
Vaccinia virus capping enzyme complexed with sah (monoclinic form)
4CKC · MRNA-capping enzyme catalytic subunit: “Vaccinia virus capping enzyme complexed with sah (monoclinic form)”. X-ray diffraction, 1 ligand (SAH), 20 pockets (best druggability 0.86). MolNFT v1 #88089 on GenesisL1: 3D structure…
- PDB
- 4CKC
- Type
- protein
- Length
- 2,207 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
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 30% 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 | 819 | 27% helix, 35% strand | P04298 |
| B | MRNA-capping enzyme regulatory subunit | protein | 284 | 43% helix, 14% strand | P04318 |
| D | MRNA-capping enzyme catalytic subunit (EC 3.1.3.33, 2.7.7.50, 2.1.1.56) | protein | 821 | 27% helix, 35% strand | P04298 |
| E | MRNA-capping enzyme regulatory subunit | protein | 283 | 43% helix, 14% strand | P04318 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.86 | 0.86 | 124 | empty |
| 2 | 1058 | 0.84 | 0.85 | 99 | SAH |
| 3 | 1004 | 0.83 | 0.84 | 95 | empty |
| 4 | 1129 | 0.83 | 0.84 | 108 | SAH |
| 5 | 265 | 0.75 | 0.88 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1570 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1561 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CKC · Vaccinia virus capping enzyme complexed with SAH (monoclinic form) · 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 P04298
- Every structure of UniProt P04318
- Elsewhere: RCSB PDB 4CKC · PDBe 4CKC · UniProt P04298 · UniProt P04318
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