Research workbench
Na in the active site of DNA polymerase lambda
Analyse Na in the active site of DNA polymerase lambda in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PFN
- Type
- protein + DNA
- Length
- 346 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Template; Primer; Downstream primer; DNA polymerase lambda
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- DUP, NA, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template | dna | 11 | — | — |
| P | Primer | dna | 6 | — | — |
| D | Downstream primer | dna | 4 | — | — |
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 49% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains T, P, A
- NA · Sodium ion · metal · 5 copies · chains P, A, T, D
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.70 | 0.74 | 71 | NA, MG, DUP |
| 2 | 115 | 0.51 | 0.82 | 22 | empty |
| 3 | 62 | 0.51 | 0.86 | 19 | empty |
| 4 | 67 | 0.42 | 0.81 | 19 | empty |
| 5 | 62 | 0.26 | 0.73 | 20 | empty |
Interfaces
5 interfaces between chains.
- T–A · 928 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–A · 387 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 376 Ų buried · 18 hydrogen bonds · protein-nucleic
- T–P · 288 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- T–D · 189 Ų buried · 17 hydrogen bonds · nucleic-nucleic
Compared structures
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 Q9UGP5
- Elsewhere: RCSB PDB 2PFN · PDBe 2PFN · UniProt Q9UGP5
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