MolNFT v1 · #137548 · protein + DNA
Human DNA polymerase beta 8-OXOG:DC extension with dttp after 60 S
5VRZ · DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG)…: “Human DNA polymerase beta 8-OXOG:DC extension with dttp after 60 S”. X-ray diffraction, 5 ligands (TTP, PPV, MG), 3 pockets (best druggability 0.70). MolNFT v1 #137548 on GenesisL1: 3D…
- PDB
- 5VRZ
- Type
- protein + DNA
- Length
- 354 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3'); DNA…
- EC
- 2.7.7.7, 4.2.99.-
- UniProt
- P06746
- Ligands
- TTP, PPV, MG, NA, CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG) P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3') | dna | 16 | — | — |
| P | DNA (5'-D(*CP*TP*GP*AP*TP*GP*CP*GP*CP*CP*T)-3') | dna | 11 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*GP*G)-3') | dna | 5 | — | — |
| A | DNA polymerase beta (EC 2.7.7.7, 4.2.99.-) | protein | 322 | 51% helix, 14% strand | P06746 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains T, P, A
- PPV · Pyrophosphate · ligand · chains P, A
- MG · Magnesium ion · metal · 5 copies · chains P, T, A
- NA · Sodium ion · metal · chains D, A
- CL · Chloride ion · ion · 2 copies · chains T, A
- IMD · Imidazole · additive · 2 copies · 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 | 884 | 0.70 | 0.76 | 61 | MG, PPV, CL |
| 2 | 377 | 0.63 | 0.78 | 32 | empty |
| 3 | 248 | 0.60 | 0.80 | 27 | empty |
Interfaces
5 interfaces between chains.
- T–A · 729 Ų buried · 18 hydrogen bonds · protein-nucleic
- P–A · 545 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 490 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- D–A · 394 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–D · 233 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, 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 5VRZ · PDBe 5VRZ · UniProt P06746
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