MolNFT v1 · #110659 · protein
I304V 3D polymerase mutant of emcv
4Y3C: “I304V 3D polymerase mutant of emcv”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.73). MolNFT v1 #110659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Y3C
- Type
- protein
- Length
- 2,760 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3D polymerase
- EC
- 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P12296
- Ligands
- CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 3D polymerase (EC 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 460 | 41% helix, 17% strand | P12296 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.73 | 0.77 | 99 | GOL |
| 2 | 883 | 0.72 | 0.76 | 88 | empty |
| 3 | 731 | 0.71 | 0.77 | 81 | empty |
| 4 | 879 | 0.71 | 0.76 | 89 | empty |
| 5 | 817 | 0.70 | 0.76 | 76 | empty |
Interfaces
8 interfaces between chains.
- D–F · 1125 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 622 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 601 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 450 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4Y3C · I304V 3D polymerase mutant of EMCV · 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 P12296
- Elsewhere: RCSB PDB 4Y3C · PDBe 4Y3C · UniProt P12296
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