Research workbench
Crystal structure of motavizumab Fab bound to peptide epitope
Analyse Crystal structure of motavizumab Fab bound to peptide epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IXT
- Type
- protein
- Length
- 894 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Motavizumab Fab light chain; Motavizumab Fab heavy chain; Fusion glycoprotein F1
- UniProt
- P03420
- Ligands
- ACE, NH2
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Motavizumab Fab light chain | protein | 211 | 5% helix, 55% strand | — |
| H | Motavizumab Fab heavy chain | protein | 213 | 7% helix, 54% strand | — |
| P, C | Fusion glycoprotein F1 | protein | 24 | 75% helix, 0% strand | P03420 |
| B | Motavizumab Fab light chain | protein | 210 | 5% helix, 55% strand | — |
| A | Motavizumab Fab heavy chain | protein | 212 | 7% helix, 54% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains P, C
- NH2 · Amino group · ion · 2 copies · chains P, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains H, P, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.71 | 0.79 | 70 | empty |
| 2 | 122 | 0.49 | 0.80 | 26 | empty |
| 3 | 156 | 0.41 | 0.74 | 23 | empty |
| 4 | 119 | 0.41 | 0.76 | 18 | empty |
| 5 | 134 | 0.39 | 0.74 | 21 | empty |
Interfaces
10 interfaces between chains.
- L–H · 1716 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1703 Ų buried · 14 hydrogen bonds · protein-protein
- H–P · 501 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 494 Ų buried · 5 hydrogen bonds · protein-protein
- H–A · 409 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3IXT · Crystal Structure of Motavizumab Fab Bound to Peptide Epitope · the same entry in another collection · chain L against L, 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 P03420
- Elsewhere: RCSB PDB 3IXT · PDBe 3IXT · UniProt P03420
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