MolNFT v1 · #110269 · protein + DNA
Human DNA polymerase lambda- mgdttp binary and complex with 6 paired DNA
4XRH: “Human DNA polymerase lambda- mgdttp binary and complex with 6 paired DNA”. X-ray diffraction, 2 ligands (TTP, MG), 4 pockets (best druggability 0.69). MolNFT v1 #110269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XRH
- Type
- protein + DNA
- Length
- 502 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'); DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3')
- EC
- 2.7.7.7
- UniProt
- Q9UGP5
- Ligands
- TTP, MG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase lambda (EC 2.7.7.7) | protein | 247 | 42% helix, 22% strand | Q9UGP5 |
| A | DNA polymerase lambda (EC 2.7.7.7) | protein | 243 | 40% helix, 22% strand | Q9UGP5 |
| P | DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') | dna | 6 | — | — |
| T | DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.69 | 0.90 | 26 | empty |
| 2 | 655 | 0.67 | 0.76 | 58 | empty |
| 3 | 50 | 0.39 | 0.81 | 18 | empty |
| 4 | 64 | 0.28 | 0.73 | 15 | TTP |
Interfaces
4 interfaces between chains.
- B–T · 581 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–A · 548 Ų buried · 4 hydrogen bonds · protein-protein
- B–P · 525 Ų buried · 17 hydrogen bonds · protein-nucleic
- P–T · 285 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XRH · Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 4XRH · PDBe 4XRH · UniProt Q9UGP5
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