Research workbench
Ternary crystal structures of a human DNA polymerase lambda in complex with DNA and (-)3TC-tp.
Analyse Ternary crystal structures of a human DNA polymerase lambda in complex with DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K4H
- Type
- protein + DNA
- Length
- 1,394 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- 1RZ, CA
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 327 | 48% helix, 13% strand | Q9UGP5 |
| B, F, J, N | DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
| C, G, K, O | DNA (5'-D(*CP*AP*GP*TP*AP*C)-3') | dna | 6 | — | — |
| D, H, L, P | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| E | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 48% helix, 13% strand | Q9UGP5 |
| I | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 332 | 48% helix, 15% strand | Q9UGP5 |
| M | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 48% helix, 15% strand | Q9UGP5 |
Ligands and binding sites
- 1RZ · Lamivudine Triphosphate · ligand · 4 copies · chains A, B, C, E, F, G, I, J, K, M, N, O
- CA · Calcium ion · metal · 23 copies · chains A, B, C, D, E, G, F, I, K, J, M, O, P, N
- ACT · Acetate ion · additive · 5 copies · chains A, F, H, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.78 | 0.81 | 126 | 1RZ, CA |
| 2 | 622 | 0.76 | 0.83 | 67 | empty |
| 3 | 611 | 0.73 | 0.81 | 60 | empty |
| 4 | 1173 | 0.70 | 0.75 | 62 | 1RZ, CA |
| 5 | 1022 | 0.70 | 0.75 | 59 | 1RZ, CA |
Interfaces
35 interfaces between chains.
- E–F · 850 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 844 Ų buried · 14 hydrogen bonds · protein-nucleic
- I–J · 625 Ų buried · 12 hydrogen bonds · protein-nucleic
- M–N · 596 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–M · 509 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4K4H · Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND… · the same entry in another collection · chain P against P, 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 4K4H · PDBe 4K4H · UniProt Q9UGP5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.