Research workbench
Structure of E. COLI NFO(ENDO IV)-H69A mutant bound to a cleaved DNA duplex containing a ALPHADA:T basepair
Analyse Structure of E. COLI NFO(ENDO IV)-H69A mutant bound to a cleaved DNA duplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K1G
- Type
- protein + DNA
- Length
- 620 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease 4; DNA (5'-D(*GP*CP*GP*TP*CP*C)-3'); DNA…
- EC
- 3.1.21.2
- UniProt
- P0A6C1
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease 4 (EC 3.1.21.2) | protein | 283 | 43% helix, 15% strand | P0A6C1 |
| B | Endonuclease 4 (EC 3.1.21.2) | protein | 279 | 44% helix, 15% strand | P0A6C1 |
| E, M | DNA (5'-D(*GP*CP*GP*TP*CP*C)-3') | dna | 6 | — | — |
| F | DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)- 3') | dna | 15 | — | — |
| H | DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3') | dna | 9 | — | — |
| N | DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)- 3') | dna | 14 | — | — |
| O | DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3') | dna | 8 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, E, B, M
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.80 | 0.96 | 32 | empty |
| 2 | 171 | 0.79 | 0.95 | 32 | empty |
| 3 | 442 | 0.65 | 0.78 | 46 | empty |
| 4 | 432 | 0.62 | 0.77 | 51 | empty |
| 5 | 177 | 0.57 | 0.81 | 17 | empty |
Interfaces
13 interfaces between chains.
- A–B · 695 Ų buried · 10 hydrogen bonds · protein-protein
- B–N · 603 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–F · 577 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–E · 471 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–M · 470 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4K1G · Structure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved DNA duplex containing a… · the same entry in another collection · chain O against O, TM-score 1.00
- P0A6C1 · AlphaFold monomer V2.0 prediction for endonuclease 4 (P0A6C1) · a predicted model of the same protein · chain B against A, 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 P0A6C1
- Elsewhere: RCSB PDB 4K1G · PDBe 4K1G · UniProt P0A6C1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.