SMTL ID : 5vjq.2 (3 other biounits)

Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin duck egg lysozyme isoform I (DEL-I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: S.31, D.32, D.99 Chain C: A.75, G.77, R.97 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:C.76, C:R.97, A:D.99 Hydrogen bonds: A:S.31 GOL.2: 8 residues within 4Å: Chain A: W.98, D.99 Chain B: H.34, Y.50, Q.89, S.91, Y.96 Ligands: CL.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.89, B:Q.89, B:S.91, B:Y.96 GOL.3: 6 residues within 4Å: Chain A: V.163, H.164 Chain B: T.164, D.165, Q.166, D.167 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.163, A:H.164, B:D.167 Water bridges: B:D.165, B:S.168 GOL.5: 6 residues within 4Å: Chain C: Q.57, I.58, N.59, W.63, A.107, W.108 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.57, C:N.59, C:W.63, C:W.108

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: D.99 Chain B: K.49, Y.50 Chain C: R.93 Ligands: GOL.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burnett, D.L. et al., Germinal center antibody mutation trajectories are determined by rapid self/foreign discrimination. Science (2018)

Release Date

2018-04-11

Peptides

HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F: A
HyHEL10 light chain Fab fragment: B
Lysozyme: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
J

HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F

HyHEL10 light chain Fab fragment

Lysozyme

Related Entries With Identical Sequence