Research workbench
Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 pa); 2.9 a resolution
Analyse Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XCN
- Type
- protein
- Length
- 2,628 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4E10 Fab light chain; 4E10 Fab heavy chain
- Ligands
- UNL, 44E, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, D, F, I, K | 4E10 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| H | 4E10 Fab heavy chain | protein | 230 | 7% helix, 52% strand | — |
| A | 4E10 Fab heavy chain | protein | 227 | 6% helix, 52% strand | — |
| C | 4E10 Fab heavy chain | protein | 228 | 6% helix, 52% strand | — |
| E | 4E10 Fab heavy chain | protein | 218 | 6% helix, 51% strand | — |
| G | 4E10 Fab heavy chain | protein | 222 | 7% helix, 54% strand | — |
| J | 4E10 Fab heavy chain | protein | 219 | 5% helix, 54% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 6 copies · chains L, H, B, A, D, C, F, E, I, G, K, J
- 44E · (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate · ligand · 2 copies · chains H, A
- PO4 · Phosphate ion · ion · 3 copies · chains C, E, J
- GOL · Glycerol · additive · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.78 | 0.84 | 80 | empty |
| 2 | 1161 | 0.73 | 0.76 | 115 | empty |
| 3 | 454 | 0.68 | 0.80 | 51 | empty |
| 4 | 377 | 0.61 | 0.77 | 48 | UNL |
| 5 | 316 | 0.61 | 0.78 | 40 | empty |
Interfaces
22 interfaces between chains.
- L–H · 1711 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 1648 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 1632 Ų buried · 10 hydrogen bonds · protein-protein
- F–E · 1609 Ų buried · 10 hydrogen bonds · protein-protein
- K–J · 1601 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4XCN · Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA); 2.9 A… · 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 4XCN · PDBe 4XCN
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