Research workbench
Crystal structure of human 4E10 Fab crystalized in the presence of phosphatidylethanolamine (06:0 pe)
Analyse Crystal structure of human 4E10 Fab crystalized in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XBP
- Type
- protein
- Length
- 1,750 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4E10 Fab light chain; 4E10 Fab heavy chain
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, D | 4E10 Fab light chain | protein | 214 | 6% helix, 50% strand | — |
| H, C | 4E10 Fab heavy chain | protein | 224 | 5% helix, 53% strand | — |
| A | 4E10 Fab heavy chain | protein | 222 | 5% helix, 53% strand | — |
| F | 4E10 Fab light chain | protein | 213 | 8% helix, 50% strand | — |
| E | 4E10 Fab heavy chain | protein | 225 | 5% helix, 53% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.83 | 0.84 | 111 | empty |
| 2 | 591 | 0.72 | 0.80 | 65 | empty |
| 3 | 497 | 0.71 | 0.81 | 72 | empty |
| 4 | 1112 | 0.70 | 0.74 | 101 | empty |
| 5 | 610 | 0.68 | 0.77 | 69 | empty |
Interfaces
17 interfaces between chains.
- L–H · 1651 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 1638 Ų buried · 10 hydrogen bonds · protein-protein
- F–E · 1588 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 1581 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 330 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4XBP · Crystal structure of human 4E10 Fab crystalized in the presence of… · 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
- Elsewhere: RCSB PDB 4XBP · PDBe 4XBP
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