MolNFT v1 · #97127 · protein + DNA
Ternary crystal structures of human DNA polymerase lambda in complex with DNA and L-dctp.
4K4G: “Ternary crystal structures of human DNA polymerase lambda in complex with DNA and L-dctp.”. X-ray diffraction, 2 ligands (1S0, CA), 19 pockets (best druggability 0.78). MolNFT v1 #97127 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4K4G
- Type
- protein + DNA
- Length
- 1,384 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
- 1S0, CA
- Pockets
- 19 · 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 | 322 | 49% helix, 12% 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 | 323 | 49% helix, 13% strand | Q9UGP5 |
| I | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 327 | 47% helix, 15% strand | Q9UGP5 |
| M | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 328 | 48% helix, 15% strand | Q9UGP5 |
Ligands and binding sites
- 1S0 · 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one · ligand · 4 copies · chains A, B, C, E, F, G, I, J, K, M, N, O
- CA · Calcium ion · metal · 22 copies · chains A, C, D, B, E, G, F, I, K, J, L, M, P, O
- ACT · Acetate ion · additive · 4 copies · chains B, D, M, N, I, F, H
- CAC · Cacodylate ion · additive · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.78 | 0.80 | 88 | CA |
| 2 | 820 | 0.73 | 0.78 | 56 | empty |
| 3 | 864 | 0.72 | 0.77 | 58 | 1S0, CA |
| 4 | 860 | 0.72 | 0.77 | 50 | 1S0, CA |
| 5 | 568 | 0.71 | 0.80 | 60 | empty |
Interfaces
35 interfaces between chains.
- E–F · 837 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 831 Ų buried · 9 hydrogen bonds · protein-nucleic
- I–J · 615 Ų buried · 11 hydrogen bonds · protein-nucleic
- M–N · 598 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–M · 495 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4K4G · Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. · 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 4K4G · PDBe 4K4G · UniProt Q9UGP5
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