SMTL ID : 5xhg.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.93, T.94 Chain B: R.50, R.59 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Water bridges: B:R.50, B:R.50, B:R.59 Salt bridges: B:R.50, B:R.59 Hydrogen bonds: A:T.94, A:T.94 SO4.7: 3 residues within 4Å: Chain B: N.206, K.208, K.213 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.206 Water bridges: B:K.208, B:K.208, B:K.213 Salt bridges: B:K.208, B:K.213

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

EDO.2: 6 residues within 4Å: Chain A: Y.87, F.98, G.99, Q.100 Chain B: G.44, L.45 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:M.4, A:M.4, A:F.98, A:Q.100 Hydrogen bonds: B:L.45 EDO.3: 6 residues within 4Å: Chain A: T.164, E.165, D.167 Chain B: V.170, H.171, T.172 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.170, A:D.167 Water bridges: B:T.172, B:T.172, A:T.164 EDO.4: 2 residues within 4Å: Chain A: S.159, E.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.159 Water bridges: A:E.161 EDO.5: 6 residues within 4Å: Chain A: S.114, V.115, F.116, K.207 Chain B: T.138, T.142 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.138, B:T.138, A:S.114 Water bridges: A:S.114, A:V.115 EDO.8: 5 residues within 4Å: Chain B: S.25, G.26, F.27, N.28, N.77 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.26, B:N.28, B:N.77 EDO.9: 8 residues within 4Å: Chain B: R.38, Q.39, A.40, K.43, G.44, L.45, E.46, E.89 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.38, B:A.40, B:G.44 Water bridges: B:R.38, B:G.44 EDO.10: 2 residues within 4Å: Chain B: G.16, S.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.17, B:S.17

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

PEG.6: 10 residues within 4Å: Chain A: I.117, F.118, P.119, F.209, E.213, C.214 Chain B: A.132, P.133, S.134, S.135 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:A.132, A:P.119 Hydrogen bonds: A:E.213

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
C

B
D

polypeptide(L)

polypeptide(H)

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