MolNFT v1 · #168225 · protein
Crystal structure of the Fab fragment of humanized 5C8 antibody containing the fluorescent non-canonical amino acid L-(7- hydroxycoumarin-4-YL)ETHYLGLYCINE in complex with CD40L at pH 6.8
6W9G · CD40 ligand: “Crystal structure of the Fab fragment of humanized 5C8 antibody containing the fluorescent non-canonical…”. X-ray diffraction, 5 ligands (TMO, ETE, MAN), 17 pockets (best druggability 0.73). MolNFT v1 #168225 on…
- PDB
- 6W9G
- Type
- protein
- Length
- 1,696 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD40 ligand; 5C8* Fab (heavy chain); 5C8* Fab (light chain)
- UniProt
- P29965
- Ligands
- TMO, ETE, MAN, NAG, BMA
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CD40 ligand | protein | 137 | 2% helix, 55% strand | P29965 |
| C | CD40 ligand | protein | 139 | 2% helix, 55% strand | P29965 |
| H | 5C8* Fab (heavy chain) | protein | 212 | 8% helix, 52% strand | — |
| L | 5C8* Fab (light chain) | protein | 215 | 6% helix, 51% strand | — |
| K | 5C8* Fab (heavy chain) | protein | 213 | 8% helix, 53% strand | — |
| M, Y | 5C8* Fab (light chain) | protein | 216 | 6% helix, 51% strand | — |
| X | 5C8* Fab (heavy chain) | protein | 211 | 10% helix, 55% strand | — |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 21 copies · chains A, B, H, C, K, X, L, M, Y
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · 3 copies · chains A, B, K, M
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains X, H, K
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, X, Y, B, H, L, C, K, M
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains X, H, K
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C, H, L, Y
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.73 | 0.79 | 96 | TRS, TMO |
| 2 | 636 | 0.72 | 0.80 | 76 | PEG, TMO |
| 3 | 370 | 0.70 | 0.82 | 51 | empty |
| 4 | 78 | 0.60 | 0.89 | 26 | empty |
| 5 | 72 | 0.57 | 0.88 | 24 | empty |
Interfaces
18 interfaces between chains.
- X–Y · 1718 Ų buried · 16 hydrogen bonds · protein-protein
- K–M · 1714 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1665 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1027 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1018 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 5 glycan, 3 modified (disulfide, N-glycosylation, nonstandard, glycosylation).
Compared structures
- 6W9G · Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P29965 · AlphaFold monomer V2.0 prediction for CD40 ligand (P29965) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P29965
- Elsewhere: RCSB PDB 6W9G · PDBe 6W9G · UniProt P29965
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