Research workbench
Gfi-1 zinc fingers 3-5 complexed with DNA
Analyse Gfi-1 zinc fingers 3-5 complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2KMK
- Type
- protein + DNA
- Length
- 114 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger protein gfi-1; DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)…
- UniProt
- Q07120
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.56
Structure
solution nmr · 3 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger protein gfi-1 | protein | 82 | 43% helix, 15% strand | Q07120 |
| B | DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)- 3') | dna | 16 | — | — |
| C | DNA (5'-D(*TP*AP*GP*GP*CP*AP*GP*TP*GP*AP*TP*TP*TP*AP*TP*G)- 3') | dna | 16 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.56 | 0.81 | 19 | empty |
| 2 | 92 | 0.42 | 0.78 | 16 | empty |
| 3 | 76 | 0.39 | 0.78 | 15 | empty |
| 4 | 50 | 0.24 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 852 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 740 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- A–C · 520 Ų buried · 9 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 Q07120
- Elsewhere: RCSB PDB 2KMK · PDBe 2KMK · UniProt Q07120
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.