MolNFT v1 · #136773 · protein + DNA
PRDM9-allele-C ZNF8-13
5V3G · DNA (5'- D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*…: “PRDM9-allele-C ZNF8-13”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.68). MolNFT v1 #136773 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5V3G
- Type
- protein + DNA
- Length
- 448 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*TP*GP*CP*CP*C)- 3'); DNA (5'…
- EC
- 2.1.1.43
- UniProt
- D9IWL3
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, B | DNA (5'- D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*TP*GP*CP*CP*C)- 3') | dna | 21 | — | — |
| F, C | DNA (5'- D(*AP*GP*GP*GP*CP*AP*AP*CP*GP*CP*TP*CP*AP*CP*TP*GP*GP*GP*GP*TP*C)- 3') | dna | 21 | — | — |
| D | Pr domain zinc finger protein 9 (EC 2.1.1.43) | protein | 170 | 39% helix, 15% strand | D9IWL3 |
| A | Pr domain zinc finger protein 9 (EC 2.1.1.43) | protein | 168 | 40% helix, 12% strand | D9IWL3 |
| G | Pr domain zinc finger protein 9 (EC 2.1.1.43) | protein | 26 | 35% helix, 15% strand | D9IWL3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 13 copies · chains D, A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.68 | 0.81 | 41 | empty |
| 2 | 134 | 0.65 | 0.88 | 22 | empty |
| 3 | 99 | 0.64 | 0.90 | 22 | empty |
| 4 | 306 | 0.63 | 0.80 | 39 | empty |
| 5 | 101 | 0.63 | 0.89 | 21 | empty |
Interfaces
10 interfaces between chains.
- C–A · 1801 Ų buried · 39 hydrogen bonds · protein-nucleic
- F–D · 1800 Ų buried · 42 hydrogen bonds · protein-nucleic
- E–D · 979 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 936 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- B–C · 932 Ų buried · 91 hydrogen bonds · nucleic-nucleic
Compared structures
- 5V3G · PRDM9-allele-C ZnF8-13 · the same entry in another collection · chain E against E, 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 D9IWL3
- Elsewhere: RCSB PDB 5V3G · PDBe 5V3G · UniProt D9IWL3
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