MolNFT v1 · #36159 · protein
Bacteriophage PHI29 DNA polymerase bound to terminal protein
2EX3: “Bacteriophage PHI29 DNA polymerase bound to terminal protein”. X-ray diffraction, 1 ligand (PB), 20 pockets (best druggability 0.83). MolNFT v1 #36159 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2EX3
- Type
- protein
- Length
- 4,596 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA terminal protein
- EC
- 2.7.7.7
- UniProt
- P03680, P03681
- Ligands
- PB
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | DNA polymerase (EC 2.7.7.7) | protein | 570 | 29% helix, 34% strand | P03680 |
| B, D, F, H, J, L | DNA terminal protein | protein | 196 | 64% helix, 4% strand | P03681 |
Ligands and binding sites
- PB · Lead (II) ion · metal · 16 copies · chains A, I, C, G, E, K
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 | 886 | 0.83 | 0.85 | 101 | PB |
| 2 | 1058 | 0.82 | 0.83 | 110 | empty |
| 3 | 1132 | 0.81 | 0.82 | 101 | empty |
| 4 | 1198 | 0.80 | 0.81 | 107 | empty |
| 5 | 889 | 0.80 | 0.82 | 74 | empty |
Interfaces
20 interfaces between chains.
- C–D · 2396 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2396 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 2376 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2363 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 2286 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 2EX3 · Bacteriophage phi29 DNA polymerase bound to terminal protein · 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 P03680
- Every structure of UniProt P03681
- Elsewhere: RCSB PDB 2EX3 · PDBe 2EX3 · UniProt P03680 · UniProt P03681
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