MolNFT v1 · #94244 · protein + DNA
Crystal structure of human PDGF-bb in complex with a modified nucleotide aptamer (somamer SL5)
4HQU · Platelet-derived growth factor subunit B: “Crystal structure of human PDGF-bb in complex with a modified nucleotide aptamer (somamer SL5)”. X-ray diffraction, 3 ligands (PE6, NA, MG), 1 pocket (best druggability 0.34). MolNFT v1…
- PDB
- 4HQU
- Type
- protein + DNA
- Length
- 118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet-derived growth factor subunit B; Somamer SL5
- UniProt
- P01127
- Ligands
- PE6, NA, MG
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet-derived growth factor subunit B | protein | 95 | 4% helix, 63% strand | P01127 |
| C | Somamer SL5 | dna | 23 | — | — |
Ligands and binding sites
- PE6 · Phosphoryl-hexaethylene glycol · ligand · chains C
- NA · Sodium ion · metal · chains C
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.34 | 0.76 | 9 | empty |
Interfaces
1 interface between chains.
- A–C · 918 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified, 3 disulfide, 2 covalent (nucleotide modification, disulfide, covalent ligand).
Compared structures
- 4HQU · Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer (SOMAmer… · the same entry in another collection · chain A against A, TM-score 1.00
- P01127 · AlphaFold monomer V2.0 prediction for platelet-derived growth factor subunit B (P01127) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P01127
- Elsewhere: RCSB PDB 4HQU · PDBe 4HQU · UniProt P01127
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