MolNFT v1 · #181624 · protein + DNA
Pre-catalytic quaternary complex of DNA polymerase lambda with bound complementary dsb substrate and incoming dumpnpp
7M0D: “Pre-catalytic quaternary complex of DNA polymerase lambda with bound complementary dsb substrate and incoming…”. X-ray diffraction, 5 ligands (DUP, K, NA), 8 pockets (best druggability 0.79). MolNFT v1 #181624 on GenesisL1: 3D…
- PDB
- 7M0D
- Type
- protein + DNA
- Length
- 721 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase lambda; DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- DUP, K, NA, MG, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 339 | 49% helix, 15% strand | Q9UGP5 |
| G, K | DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') | dna | 7 | — | — |
| F, J | DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') | dna | 6 | — | — |
| H, L | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| B | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 340 | 49% helix, 16% strand | Q9UGP5 |
| I, E | DNA (5'-D(*AP*CP*TP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 2 copies · chains A, G, F, B, K, J
- K · Potassium ion · metal · 6 copies · chains A, H, B, L
- NA · Sodium ion · metal · 5 copies · chains A, F, B, J, K, L
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, F, B, J
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, F, B, J
- CIT · Citric acid · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.79 | 0.81 | 88 | empty |
| 2 | 399 | 0.71 | 0.82 | 36 | EDO |
| 3 | 745 | 0.70 | 0.77 | 47 | DUP, MG, K, TRS, EDO |
| 4 | 747 | 0.69 | 0.77 | 50 | DUP, NA, MG, K, FMT, TRS, EDO |
| 5 | 382 | 0.68 | 0.81 | 34 | empty |
Interfaces
23 interfaces between chains.
- B–K · 569 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–G · 544 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 423 Ų buried · 10 hydrogen bonds · protein-protein
- B–L · 396 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–F · 389 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7M0D · Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9UGP5 · AlphaFold monomer V2.0 prediction for DNA polymerase lambda (Q9UGP5) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 7M0D · PDBe 7M0D · UniProt Q9UGP5
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