MolNFT v1 · #46857 · protein + DNA
Ternary complex of human DNA polymerase
2OH2 · 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3': “Ternary complex of human DNA polymerase”. X-ray diffraction, 2 ligands (TTP, MG), 11 pockets (best druggability 0.77). MolNFT v1 #46857 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2OH2
- Type
- protein + DNA
- Length
- 918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- Q9UBT6
- Ligands
- TTP, MG
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3' | dna | 10 | — | — |
| Q | 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3' | dna | 13 | — | — |
| P | 5'-D(*GP*GP*G*GP*GP*AP*AP*GP*GP*AP*CP*CP*C)-3' | dna | 12 | — | — |
| T | 5'-D(*TP*T*CP*CP*AP*GP*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3' | dna | 15 | — | — |
| A | DNA polymerase kappa (EC 2.7.7.7) | protein | 428 | 48% helix, 17% strand | Q9UBT6 |
| B | DNA polymerase kappa (EC 2.7.7.7) | protein | 440 | 44% helix, 17% strand | Q9UBT6 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains S, Q, A, P, T, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.77 | 0.86 | 45 | empty |
| 2 | 703 | 0.77 | 0.82 | 47 | empty |
| 3 | 802 | 0.76 | 0.80 | 77 | TTP |
| 4 | 76 | 0.74 | 0.97 | 22 | empty |
| 5 | 270 | 0.71 | 0.86 | 38 | MG, TTP |
Interfaces
7 interfaces between chains.
- T–B · 943 Ų buried · 20 hydrogen bonds · protein-nucleic
- Q–A · 940 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 890 Ų buried · 9 hydrogen bonds · protein-protein
- S–A · 607 Ų buried · 18 hydrogen bonds · protein-nucleic
- P–B · 605 Ų buried · 14 hydrogen bonds · protein-nucleic
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 Q9UBT6
- Elsewhere: RCSB PDB 2OH2 · PDBe 2OH2 · UniProt Q9UBT6
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