Research workbench
Crystal structure of human 4E10 Fab in complex with phosphatidylglycerol (06:0 pg)
Analyse Crystal structure of human 4E10 Fab in complex with phosphatidylglycerol (06:0… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XCY
- Type
- protein
- Length
- 2,612 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, 44G
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, D, F | 4E10 Fab light chain | protein | 214 | 6% helix, 49% strand | — |
| H | 4E10 Fab heavy chain | protein | 224 | 4% helix, 50% strand | — |
| A | 4E10 Fab heavy chain | protein | 228 | 4% helix, 49% strand | — |
| C | 4E10 Fab heavy chain | protein | 221 | 4% helix, 52% strand | — |
| E | 4E10 Fab heavy chain | protein | 223 | 5% helix, 49% strand | — |
| I | 4E10 Fab light chain | protein | 211 | 7% helix, 49% strand | — |
| G | 4E10 Fab heavy chain | protein | 216 | 4% helix, 52% strand | — |
| K | 4E10 Fab light chain | protein | 212 | 7% helix, 49% strand | — |
| J | 4E10 Fab heavy chain | protein | 221 | 4% helix, 51% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 5 copies · chains L, H, B, A, D, C, F, E, K, J
- 44G · (2S)-3-{[(R)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate · ligand · 2 copies · chains H, A, E
- GOL · Glycerol · additive · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.80 | 0.84 | 86 | empty |
| 2 | 320 | 0.79 | 0.89 | 43 | empty |
| 3 | 669 | 0.74 | 0.80 | 55 | empty |
| 4 | 766 | 0.70 | 0.77 | 74 | empty |
| 5 | 605 | 0.68 | 0.78 | 50 | empty |
Interfaces
21 interfaces between chains.
- K–J · 1691 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 1687 Ų buried · 12 hydrogen bonds · protein-protein
- L–H · 1664 Ų buried · 11 hydrogen bonds · protein-protein
- F–E · 1636 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 1594 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4XCY · Crystal structure of human 4E10 Fab in complex with phosphatidylglycerol (06:0 PG) · 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 4XCY · PDBe 4XCY
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.