MolNFT v1 · #152667 · protein + DNA
Post-catalytic complex of human DNA polymerase mu with templating adenine and mn-8OXODGMP
6IPD · DNA-directed DNA/RNA polymerase mu: “Post-catalytic complex of human DNA polymerase mu with templating adenine and mn-8OXODGMP”. X-ray diffraction, 3 ligands (OXD, MN, NA), 2 pockets (best druggability 0.73). MolNFT v1 #152667 on…
- PDB
- 6IPD
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed DNA/RNA polymerase mu; DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9NP87
- Ligands
- OXD, MN, NA
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed DNA/RNA polymerase mu (EC 2.7.7.7) | protein | 326 | 52% helix, 14% strand | Q9NP87 |
| T | DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3') | dna | 9 | — | — |
| P | DNA (5'-D(*CP*GP*TP*AP*(8OG))-3') | dna | 5 | — | — |
| D | DNA (5'-D(P*GP*CP*CP*G)-3') | dna | 4 | — | — |
Ligands and binding sites
- OXD · Oxalic acid · ligand · chains A, P
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
- NA · Sodium ion · metal · 2 copies · chains A, P, T
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, T, P
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.73 | 0.76 | 54 | MN, OXD, EDO |
| 2 | 85 | 0.43 | 0.80 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–T · 700 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 579 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 370 Ų buried · 15 hydrogen bonds · protein-nucleic
- T–P · 250 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- T–D · 194 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6IPD · Post-catalytic Complex of Human DNA Polymerase Mu with Templating Adenine and Mn-8oxodGMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NP87 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9NP87) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9NP87
- Elsewhere: RCSB PDB 6IPD · PDBe 6IPD · UniProt Q9NP87
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