Research workbench
Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with blocked excited state proton transfer and in complex with its antigen, CD40L
Analyse Crystal structure of a Fab variant containing a fluorescent noncanonical amino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SGM
- Type
- protein
- Length
- 1,693 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, NAG
- Pockets
- 18 · best druggability 0.68
Structure
x-ray diffraction · 9 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD40 ligand | protein | 137 | 2% helix, 55% strand | P29965 |
| B | CD40 ligand | protein | 140 | 2% helix, 54% strand | P29965 |
| C | CD40 ligand | protein | 137 | 2% helix, 55% strand | P29965 |
| H | 5C8* Fab heavy chain | protein | 211 | 8% helix, 53% strand | — |
| L | 5C8* Fab light chain | protein | 208 | 1% helix, 50% strand | — |
| K | 5C8* Fab heavy chain | protein | 213 | 10% helix, 53% strand | — |
| M | 5C8* Fab light chain | protein | 217 | 6% helix, 50% strand | — |
| X | 5C8* Fab heavy chain | protein | 214 | 10% helix, 50% strand | — |
| Y | 5C8* Fab light chain | protein | 216 | 6% helix, 50% strand | — |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 3 copies · chains L, M, Y
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 13 copies · chains A, B, C, H, L, K, M, X, Y
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.68 | 0.82 | 52 | empty |
| 2 | 529 | 0.68 | 0.78 | 66 | empty |
| 3 | 359 | 0.68 | 0.81 | 55 | empty |
| 4 | 186 | 0.56 | 0.80 | 28 | TRS |
| 5 | 308 | 0.53 | 0.75 | 41 | empty |
Interfaces
18 interfaces between chains.
- X–Y · 1721 Ų buried · 17 hydrogen bonds · protein-protein
- K–M · 1707 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1663 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1006 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1000 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan, 3 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 7SGM · Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with… · 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 7SGM · PDBe 7SGM · UniProt P29965
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