MolNFT v1 · #156552 · protein + DNA
Human DNA polymerase eta in a non-productive ternary complex with MG2+ and dtmpnpp oppositing cda
6M7U: “Human DNA polymerase eta in a non-productive ternary complex with MG2+ and dtmpnpp oppositing cda”. X-ray diffraction, 4 ligands (1FZ, NI, MG), 5 pockets (best druggability 0.81). MolNFT v1 #156552 on GenesisL1: 3D structure…
- PDB
- 6M7U
- Type
- protein + DNA
- Length
- 436 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- 1FZ, NI, MG, CL
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 417 | 42% helix, 19% strand | Q9Y253 |
| P | DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3') | dna | 8 | — | — |
| T | DNA (5'-D(*AP*TP*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- 1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · chains A, P, T
- NI · Nickel (II) ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.81 | 0.85 | 75 | 1FZ |
| 2 | 461 | 0.73 | 0.83 | 39 | CL |
| 3 | 59 | 0.43 | 0.82 | 15 | empty |
| 4 | 54 | 0.42 | 0.83 | 9 | empty |
| 5 | 94 | 0.38 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 691 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–P · 522 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 420 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6M7U · Human DNA polymerase eta in a non-productive ternary complex with Mg2+ and dTMPNPP… · the same entry in another collection · chain A against A, 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 Q9Y253
- Elsewhere: RCSB PDB 6M7U · PDBe 6M7U · UniProt Q9Y253
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