› 6w9g

X-ray diffraction
1.82Å resolution

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

Released:
DOI: 10.2210/pdb6w9g/pdb
PDB entry 6w9g coloured by chain, front view.
PDB entry 6w9g coloured by chain, side view.
PDB entry 6w9g coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore.
Henderson JN, Simmons CR, Fahmi NE, Jeffs JW, Borges CR, Mills JH
Biochemistry 59 3401-3410 (2020)
PMID: 32845612

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-210999 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
CD40 ligand, soluble form Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 146 amino acids
Theoretical weight: 15.81 KDa
Source organism: Homo sapiens
Expression system: Komagataella phaffii GS115
UniProt:
  • Canonical: P29965 (Residues: 116-261; Coverage: 56%)
Gene names: CD40L, CD40LG, TNFSF5, TRAP
Sequence domains: TNF(Tumour Necrosis Factor) family
5c8* Fab (heavy chain) Chains: H, K, X
Molecule details ›
Chains: H, K, X
Length: 226 amino acids
Theoretical weight: 24.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
5c8* Fab (light chain) Chains: L, M, Y
Molecule details ›
Chains: L, M, Y
Length: 218 amino acids
Theoretical weight: 24.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
5 bound ligands:
Ligand PEG 8 x PEG
Ligand TRS 2 x TRS
Ligand TMO 21 x TMO
Ligand ETE 3 x ETE
Ligand 1PE 1 x 1PE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2
Unit cell:
a: 226.677Å b: 131.2Å c: 97.56Å
α: 90° β: 108.82° γ: 90°
R-values:
R R work R free
0.18 0.179 0.207
Expression systems:
  • Komagataella phaffii GS115
  • Escherichia coli

Quick links

Citations

5 citation in other articles

To twist or not to twist: From chromophore structure to dynamics inside engineered photoconvertible and photoswitchable fluorescent proteins.
Krueger et al. (2023)
4 more

2 mentions without citation

Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore.
Henderson et al. (2020)
1 more