SMTL ID : 6w9g.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 15 residues within 4Å: Chain A: T.20, S.21, V.22, C.79, E.87, F.123, N.125 Chain H: K.38, E.46, E.62, K.63, F.64, E.89, D.90 Chain I: X.98 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:K.38, H:E.89 NAG-NAG-BMA-MAN-MAN-MAN.2: 15 residues within 4Å: Chain B: T.20, S.21, V.22, C.79, E.87, F.123, N.125 Chain D: K.38, E.46, E.62, K.63, F.64, E.89, D.90 Chain E: X.98 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.38, D:E.89 NAG-NAG-BMA-MAN-MAN-MAN.3: 16 residues within 4Å: Chain C: T.20, S.21, V.22, C.79, E.87, F.123, N.125 Chain F: K.38, E.46, E.62, K.63, F.64, R.87, E.89, D.90 Chain G: X.98 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.38, F:E.46, F:R.87, F:E.89 Water bridges: F:E.46

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

PEG.4: 4 residues within 4Å: Chain A: V.22, Q.45, K.81, F.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.45 PEG.9: 3 residues within 4Å: Chain B: Q.45, K.81, F.123 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.45 PEG.12: 2 residues within 4Å: Chain C: Y.31, M.33 1 PLIP interactions: 1 interactions with chain C Water bridges: C:M.33 PEG.13: 5 residues within 4Å: Chain C: V.22, K.44, Q.45, K.81, F.123 No protein-ligand interaction detected (PLIP) PEG.18: 6 residues within 4Å: Chain D: G.42 Chain E: A.9, T.10, Y.91, G.104, G.105 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:T.10, E:T.10, E:Y.91, D:G.42 PEG.34: 6 residues within 4Å: Chain I: A.9, T.10, Y.91, G.104, G.105, K.107 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:T.10, I:Y.91, I:Y.91 PEG.35: 2 residues within 4Å: Chain I: E.17, R.18 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.18 Water bridges: I:R.18 PEG.36: 5 residues within 4Å: Chain I: E.147, A.148, T.201, H.202, Q.203 2 PLIP interactions: 2 interactions with chain I Water bridges: I:H.202, I:Q.203

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

TRS.5: 6 residues within 4Å: Chain A: L.144, L.146 Chain B: K.145, L.146 Chain C: K.145, L.146 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:L.146, B:L.146, B:L.146, C:L.146 Water bridges: C:L.146 TRS.6: 10 residues within 4Å: Chain A: T.96, H.97, S.98, Q.106 Chain B: T.96, H.97, Q.106 Chain C: T.96, H.97, Q.106 11 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: C:T.96, C:H.97, C:Q.106, C:Q.106, A:T.96, A:H.97, A:S.99, A:Q.106, B:T.96, B:H.97, B:Q.106

21 x TMO: trimethylamine oxide(Non-covalent)

TMO.7: 5 residues within 4Å: Chain A: C.103, Q.105 Chain B: P.73 Chain D: D.57, T.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105 Water bridges: A:Q.105 TMO.10: 4 residues within 4Å: Chain B: C.63, Q.105 Chain C: P.73 Chain F: D.57 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.57 Water bridges: F:T.58 Salt bridges: F:D.57 TMO.14: 6 residues within 4Å: Chain A: P.73 Chain C: C.63, C.103, Q.105 Chain H: D.57, T.58 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain C Hydrogen bonds: H:D.57, H:T.58 Salt bridges: H:D.57 Water bridges: C:Q.105, C:Q.105 TMO.16: 6 residues within 4Å: Chain D: Q.39, Y.95 Chain E: Q.42, P.44, G.45, Q.46 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.45 TMO.17: 4 residues within 4Å: Chain D: V.2, R.98, D.106, S.107 1 PLIP interactions: 1 interactions with chain E Water bridges: E:E.59 TMO.19: 5 residues within 4Å: Chain E: S.31, S.32, T.33, Y.34, S.35 No protein-ligand interaction detected (PLIP) TMO.20: 1 residues within 4Å: Chain E: T.5 No protein-ligand interaction detected (PLIP) TMO.21: 3 residues within 4Å: Chain E: T.5, Q.6, S.7 No protein-ligand interaction detected (PLIP) TMO.22: 3 residues within 4Å: Chain A: E.14 Chain E: Y.34, Y.54 No protein-ligand interaction detected (PLIP) TMO.23: 6 residues within 4Å: Chain F: Q.39, Y.95 Chain G: Q.42, P.44, G.45, Q.46 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.45 TMO.24: 2 residues within 4Å: Chain F: K.211, D.213 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.211 Salt bridges: F:D.213 TMO.25: 3 residues within 4Å: Chain F: Q.110, G.111 Chain G: G.45 1 PLIP interactions: 1 interactions with chain F Water bridges: F:G.111 TMO.26: 5 residues within 4Å: Chain F: V.2, R.98, D.106, S.107 Chain G: E.59 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.59 TMO.27: 5 residues within 4Å: Chain G: S.31, S.32, T.33, Y.34, S.35 No protein-ligand interaction detected (PLIP) TMO.28: 2 residues within 4Å: Chain G: Y.34, Y.54 No protein-ligand interaction detected (PLIP) TMO.29: 1 residues within 4Å: Chain G: S.80 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:S.80 TMO.30: 3 residues within 4Å: Chain G: F.87, I.110, Q.170 No protein-ligand interaction detected (PLIP) TMO.32: 6 residues within 4Å: Chain H: Q.39, Y.95 Chain I: Q.42, P.44, G.45, Q.46 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.45 TMO.33: 3 residues within 4Å: Chain H: Q.110, G.111 Chain I: G.45 No protein-ligand interaction detected (PLIP) TMO.37: 5 residues within 4Å: Chain I: S.31, S.32, T.33, Y.34, S.35 1 PLIP interactions: 1 interactions with chain I Water bridges: I:S.71 TMO.38: 2 residues within 4Å: Chain I: Y.34, Y.54 No protein-ligand interaction detected (PLIP)

3 x ETE: 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-covalent)

ETE.8: 3 residues within 4Å: Chain A: P.83, G.84, F.86 No protein-ligand interaction detected (PLIP) ETE.11: 5 residues within 4Å: Chain B: K.81, P.83, G.84, R.85, F.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.84 ETE.31: 8 residues within 4Å: Chain F: G.42 Chain G: A.9, T.10, Y.91, G.104, G.105, K.107, R.146 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:T.10, G:Y.91, G:Y.91, G:R.146 Water bridges: G:T.89, G:R.146

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.15: 4 residues within 4Å: Chain C: P.83, G.84, R.85, F.86 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henderson, J.N. et al., Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore. Biochemistry (2020)

Release Date

2020-12-23

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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