Research workbench
Human DNA polymerase beta complexed with gapped DNA containing an 8-oxo-7,8-dihydro-guanine template paired with dctp
Analyse Human DNA polymerase beta complexed with gapped DNA containing an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MQ3
- Type
- protein + DNA
- Length
- 357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*GP*AP*CP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- P06746
- Ligands
- DCP, NA, MG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*CP*CP*GP*AP*CP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' | dna | 16 | — | — |
| P | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3' | dna | 10 | — | — |
| D | 5'-D(P*GP*TP*CP*GP*G)-3' | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7) | protein | 326 | 49% helix, 13% strand | P06746 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains T, P, A
- NA · Sodium ion · metal · 2 copies · chains P, A, D
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.71 | 0.77 | 57 | MG, DCP |
| 2 | 351 | 0.63 | 0.79 | 31 | empty |
| 3 | 184 | 0.54 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- T–A · 725 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 452 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- D–A · 380 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–A · 364 Ų buried · 10 hydrogen bonds · protein-nucleic
- T–D · 243 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
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 P06746
- Elsewhere: RCSB PDB 1MQ3 · PDBe 1MQ3 · UniProt P06746
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