MolNFT v1 · #156549 · protein + DNA
Human DNA polymerase eta ternary complex with MN2+ and dtmpnpp oppositing cda
6M7O: “Human DNA polymerase eta ternary complex with MN2+ and dtmpnpp oppositing cda”. X-ray diffraction, 2 ligands (1FZ, MN), 5 pockets (best druggability 0.80). MolNFT v1 #156549 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6M7O
- Type
- protein + DNA
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*AP*TP*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- 1FZ, MN
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 423 | 44% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*AP*TP*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(P*AP*GP*TP*GP*TP*GP*AP*G*(1FZ))-3') | dna | 8 | — | — |
Ligands and binding sites
- 1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · chains A, T, P
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.80 | 0.83 | 60 | MN, 1FZ |
| 2 | 485 | 0.74 | 0.83 | 42 | empty |
| 3 | 202 | 0.66 | 0.85 | 22 | empty |
| 4 | 118 | 0.54 | 0.83 | 23 | empty |
| 5 | 96 | 0.37 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 895 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 620 Ų buried · 14 hydrogen bonds · protein-nucleic
- T–P · 384 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6M7O · Human DNA polymerase eta ternary complex with Mn2+ and dTMPNPP oppositing cdA · 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 6M7O · PDBe 6M7O · UniProt Q9Y253
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