SMTL ID : 7sgm.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 6 residues within 4Å: Chain A: S.21, V.22, C.79, E.87, I.89, N.125 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.89 Hydrogen bonds: A:S.21, A:S.21, A:V.22, A:E.87, A:E.87, A:N.125 NAG.4: 7 residues within 4Å: Chain B: T.20, S.21, V.22, C.79, E.87, N.125 Ligands: PEG.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.87 Hydrogen bonds: B:S.21, B:V.22, B:E.87, B:E.87, B:E.87, B:N.125 NAG.6: 6 residues within 4Å: Chain C: T.20, S.21, V.22, C.79, E.87, N.125 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:E.87 Hydrogen bonds: C:S.21, C:V.22, C:E.87, C:E.87, C:N.125

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 6 residues within 4Å: Chain A: K.145, L.146 Chain B: K.145, L.146 Chain C: K.145, L.146 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:L.146, B:L.146, C:L.146, C:L.146 Water bridges: A:L.146

13 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 2 residues within 4Å: Chain A: G.84, F.86 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.81, A:R.85 PEG.5: 2 residues within 4Å: Chain B: G.84, F.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.84 PEG.7: 2 residues within 4Å: Chain C: G.84, F.86 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.84 PEG.8: 2 residues within 4Å: Chain D: E.62 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) PEG.9: 8 residues within 4Å: Chain D: P.131, G.138, T.140, A.141, A.142 Chain E: F.120, I.121, F.122 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:I.121, D:G.138, D:A.142 Water bridges: E:I.121 PEG.11: 2 residues within 4Å: Chain E: S.71 Ligands: TMO.10 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.71 PEG.12: 1 residues within 4Å: Chain E: R.18 No protein-ligand interaction detected (PLIP) PEG.13: 3 residues within 4Å: Chain E: Y.34, Y.54, N.57 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.57 PEG.14: 3 residues within 4Å: Chain F: L.45 Chain G: F.102, G.104 2 PLIP interactions: 2 interactions with chain F Water bridges: F:G.44, F:G.44 PEG.16: 3 residues within 4Å: Chain G: S.32, S.71 Ligands: TMO.15 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.71 PEG.17: 2 residues within 4Å: Chain H: G.44, E.46 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:G.44 Water bridges: H:K.38, H:G.44, I:D.1 PEG.19: 2 residues within 4Å: Chain I: S.71 Ligands: TMO.18 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:S.71 PEG.20: 7 residues within 4Å: Chain H: G.42 Chain I: A.9, T.10, Y.91, G.104, G.105, K.107 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:Q.43, I:T.10, I:T.10, I:Y.91 Water bridges: H:Q.39

3 x TMO: trimethylamine oxide(Non-covalent)

TMO.10: 8 residues within 4Å: Chain E: S.30, S.31, S.32, T.33, Y.34, S.35, S.71 Ligands: PEG.11 2 PLIP interactions: 2 interactions with chain E Water bridges: E:S.35, E:S.35 TMO.15: 7 residues within 4Å: Chain G: S.31, S.32, T.33, Y.34, S.35, S.71 Ligands: PEG.16 1 PLIP interactions: 1 interactions with chain G Water bridges: G:S.35 TMO.18: 6 residues within 4Å: Chain I: S.30, S.31, S.32, T.33, Y.34 Ligands: PEG.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henderson, J.N. et al., Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment. J.Mol.Biol. (2022)

Release Date

2022-02-02

Peptides

CD40 ligand: ABC
5c8* Fab heavy chain: DFH
5c8* Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
K

H
X

E
L

G
M

I
Y

CD40 ligand

5c8* Fab heavy chain

5c8* Fab light chain

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