MolNFT v1 · #66659 · protein + DNA
Ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched da
3HX0 · DNA polymerase lambda: “Ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a…”. X-ray diffraction, 3 ligands (D3T, NA, MG), 17 pockets (best druggability 0.77). MolNFT v1 #66659…
- PDB
- 3HX0
- Type
- protein + DNA
- Length
- 1,401 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3'…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- D3T, NA, MG
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 330 | 47% helix, 12% strand | Q9UGP5 |
| B, G, L, Q | 5'-D(*CP*GP*GP*CP*AP*AP*AP*TP*AP*CP*TP*G)-3' | dna | 12 | — | — |
| C, H, M, R | 5'-D(*CP*AP*GP*TP*AP*T)-3' | dna | 6 | — | — |
| D, I, N, S | 5'-D(P*GP*CP*CP*G)-3' | dna | 4 | — | — |
| F | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 329 | 47% helix, 12% strand | Q9UGP5 |
| K, P | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 327 | 46% helix, 15% strand | Q9UGP5 |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, F, G, H, K, M, P, R
- NA · Sodium ion · metal · 5 copies · chains F, H, K, M, P, R
- MG · Magnesium ion · metal · 4 copies · chains A, F, K, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.77 | 0.81 | 86 | D3T, MG, NA |
| 2 | 866 | 0.77 | 0.80 | 78 | empty |
| 3 | 884 | 0.67 | 0.74 | 56 | D3T, MG |
| 4 | 353 | 0.67 | 0.81 | 41 | D3T, NA |
| 5 | 770 | 0.64 | 0.74 | 69 | empty |
Interfaces
31 interfaces between chains.
- F–G · 907 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 883 Ų buried · 9 hydrogen bonds · protein-nucleic
- K–L · 587 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–Q · 581 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 398 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3HX0 · ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped… · the same entry in another collection · chain S against S, 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 Q9UGP5
- Elsewhere: RCSB PDB 3HX0 · PDBe 3HX0 · UniProt Q9UGP5
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