SMTL ID : 5xhg.1 (1 other biounit)

Crystal structure of Trastuzumab Fab fragment bearing Ne-(o-azidobenzyloxycarbonyl)-L-lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-1-1-mer

Ligands

1 x OAZ: (2-azidophenyl)methyl hydrogen carbonate(Covalent)

OAZ.1: 4 residues within 4Å: Chain A: V.150, A.153, K.155, H.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.150

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 1 residues within 4Å: Chain A: R.211 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.211 Salt bridges: A:R.211

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: Y.92, T.93, T.94 Chain B: R.59 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:R.59, A:Y.92 Hydrogen bonds: A:T.94, A:T.94, A:T.94 EDO.4: 6 residues within 4Å: Chain B: E.155, T.172, F.173, P.174, A.175, L.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.155, B:A.175

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

PEG.5: 6 residues within 4Å: Chain A: Y.55, S.56 Chain B: V.2, R.98, D.108, Y.109 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.56, B:R.98, B:Y.109 Water bridges: B:R.98, B:Y.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, A. et al., Extensive Survey of Antibody Invariant Positions for Efficient Chemical Conjugation Using Expanded Genetic Codes. Bioconjug. Chem. (2017)

Release Date

2017-12-20

Peptides

polypeptide(L): A
polypeptide(H): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

polypeptide(L)

polypeptide(H)

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