MolNFT v1 · #34364 · protein
Crystal structure of the Fab fragment of a R310 antibody complexed with (R)-hne-histidine adduct
2DDQ · R310 antibody heavy chain: “Crystal structure of the Fab fragment of a R310 antibody complexed with (R)-hne-histidine adduct”. X-ray diffraction, 1 ligand (HRB), 5 pockets (best druggability 0.55). MolNFT v1 #34364 on GenesisL1: 3D…
- PDB
- 2DDQ
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R310 antibody heavy chain; R310 antibody light chain
- UniProt
- Q9JL75
- Ligands
- HRB
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | R310 antibody heavy chain | protein | 211 | 6% helix, 51% strand | Q9JL75 |
| L | R310 antibody light chain | protein | 218 | 6% helix, 52% strand | — |
Ligands and binding sites
- HRB · N-acetyl-1-[(2R,3S,5R)-5-hydroxy-2-pentyltetrahydrofuran-3-yl]-L-histidine · ligand · chains H, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.55 | 0.78 | 28 | HRB |
| 2 | 331 | 0.54 | 0.74 | 52 | empty |
| 3 | 94 | 0.36 | 0.74 | 23 | empty |
| 4 | 79 | 0.33 | 0.74 | 15 | empty |
| 5 | 60 | 0.26 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- H–L · 1635 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2DDQ · Crystal Structure of the Fab fragment of a R310 antibody complexed with (R)-HNE-histidine… · the same entry in another collection · chain H against H, 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 Q9JL75
- Elsewhere: RCSB PDB 2DDQ · PDBe 2DDQ · UniProt Q9JL75
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