Research workbench
Structure of the E9 DNA polymerase from vaccinia virus in complex with manganese
Analyse Structure of the E9 DNA polymerase from vaccinia virus in complex with manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N2G
- Type
- protein
- Length
- 999 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase
- EC
- 2.7.7.7, 3.1.11.-
- UniProt
- P20509
- Ligands
- MN
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 999 | 34% helix, 26% strand | P20509 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.72 | 0.77 | 99 | empty |
| 2 | 247 | 0.70 | 0.86 | 41 | MES |
| 3 | 442 | 0.64 | 0.77 | 38 | empty |
| 4 | 324 | 0.58 | 0.76 | 28 | MN |
| 5 | 222 | 0.53 | 0.77 | 33 | GOL |
Compared structures
- 5N2G · Structure of the E9 DNA polymerase from vaccinia virus in complex with manganese · 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 P20509
- Elsewhere: RCSB PDB 5N2G · PDBe 5N2G · UniProt P20509
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