MolNFT v1 · #181625 · protein + DNA
Pre-catalytic synaptic complex of DNA polymerase lambda with gapped dsb substrate and incoming dumpnpp
7M0E: “Pre-catalytic synaptic complex of DNA polymerase lambda with gapped dsb substrate and incoming dumpnpp”. X-ray diffraction, 4 ligands (DUP, MG, NA), 14 pockets (best druggability 0.79). MolNFT v1 #181625 on GenesisL1: 3D structure…
- PDB
- 7M0E
- Type
- protein + DNA
- Length
- 1,369 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*AP*GP*C)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- Q9UGP5
- Ligands
- DUP, MG, NA, SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 52% helix, 14% strand | Q9UGP5 |
| G, K, O, T | DNA (5'-D(*CP*GP*GP*CP*AP*GP*C)-3') | dna | 7 | — | — |
| F, J, N, R | DNA (5'-D(*CP*AP*GP*TP*GP*C)-3') | dna | 6 | — | — |
| H, L, P, U | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
| B | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 324 | 52% helix, 14% strand | Q9UGP5 |
| C | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 326 | 52% helix, 14% strand | Q9UGP5 |
| D | DNA polymerase lambda (EC 2.7.7.7, 4.2.99.-) | protein | 325 | 52% helix, 14% strand | Q9UGP5 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 4 copies · chains A, G, F, B, K, J, C, O, N, D, T, R
- MG · Magnesium ion · metal · 6 copies · chains A, F, J, B, C, N, R, D
- NA · Sodium ion · metal · 4 copies · chains A, F, B, J, C, N, D, R
- SO4 · Sulfate ion · ion · 2 copies · chains A, F, J, C, N, R
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.79 | 0.82 | 64 | empty |
| 2 | 748 | 0.78 | 0.82 | 75 | SO4 |
| 3 | 721 | 0.77 | 0.82 | 80 | SO4 |
| 4 | 981 | 0.69 | 0.74 | 63 | DUP, MG |
| 5 | 440 | 0.68 | 0.80 | 35 | empty |
Interfaces
45 interfaces between chains.
- B–K · 548 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–G · 545 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–O · 544 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–T · 491 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–J · 423 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 7M0E · Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and… · the same entry in another collection · chain U against U, 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 7M0E · PDBe 7M0E · UniProt Q9UGP5
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