Research workbench
Non-helical DNA triplex forms a unique aptamer scaffold for high affinity recognition of nerve growth factor
Analyse Non-helical DNA triplex forms a unique aptamer scaffold for high affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZBN
- Type
- protein + DNA
- Length
- 252 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (28-mer); Beta-nerve growth factor
- UniProt
- P01138
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E | DNA (28-mer) | dna | 28 | — | — |
| A | Beta-nerve growth factor | protein | 97 | 0% helix, 66% strand | P01138 |
| B | Beta-nerve growth factor | protein | 99 | 3% helix, 59% strand | P01138 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.75 | 0.97 | 28 | empty |
| 2 | 311 | 0.69 | 0.83 | 43 | empty |
| 3 | 322 | 0.61 | 0.79 | 31 | empty |
| 4 | 90 | 0.37 | 0.76 | 16 | empty |
| 5 | 62 | 0.30 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1502 Ų buried · 11 hydrogen bonds · protein-protein
- E–B · 707 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 602 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–B · 366 Ų buried · 4 hydrogen bonds · protein-nucleic
- E–A · 358 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 modified, 6 disulfide (nucleotide modification, disulfide).
Compared structures
- 4ZBN · Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of… · the same entry in another collection · chain D against D, TM-score 1.00
- P01138 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01138) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P01138
- Elsewhere: RCSB PDB 4ZBN · PDBe 4ZBN · UniProt P01138
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