MolNFT v1 · #109730 · protein
Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 pa): 2.73 a resolution
4XBG · 4E10 Fab light chain: “Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 pa): 2.73 a resolution”. X-ray diffraction, 3 ligands (UNL, 44E, PO4), 20 pockets (best druggability 0.78). MolNFT v1 #109730 on…
- PDB
- 4XBG
- Type
- protein
- Length
- 2,617 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 · 9 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B, D, I | 4E10 Fab light chain | protein | 214 | 7% helix, 49% strand | — |
| H | 4E10 Fab heavy chain | protein | 230 | 5% helix, 53% strand | — |
| A | 4E10 Fab heavy chain | protein | 227 | 6% helix, 51% strand | — |
| C | 4E10 Fab heavy chain | protein | 226 | 6% helix, 53% strand | — |
| F | 4E10 Fab light chain | protein | 212 | 8% helix, 47% strand | — |
| E | 4E10 Fab heavy chain | protein | 218 | 6% helix, 52% strand | — |
| G | 4E10 Fab heavy chain | protein | 219 | 7% helix, 54% strand | — |
| K | 4E10 Fab light chain | protein | 212 | 6% helix, 50% strand | — |
| J | 4E10 Fab heavy chain | protein | 217 | 7% 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 · 3 copies · chains H, A
- PO4 · Phosphate ion · ion · 4 copies · chains C, E, G, J
- GOL · Glycerol · additive · 2 copies · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.78 | 0.84 | 78 | empty |
| 2 | 1084 | 0.75 | 0.78 | 132 | empty |
| 3 | 598 | 0.70 | 0.79 | 63 | empty |
| 4 | 670 | 0.63 | 0.74 | 61 | UNL |
| 5 | 508 | 0.61 | 0.75 | 60 | UNL |
Interfaces
22 interfaces between chains.
- L–H · 1739 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 1714 Ų buried · 11 hydrogen bonds · protein-protein
- D–C · 1644 Ų buried · 10 hydrogen bonds · protein-protein
- F–E · 1637 Ų buried · 9 hydrogen bonds · protein-protein
- K–J · 1595 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4XBG · Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA): 2.73 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 4XBG · PDBe 4XBG
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