SMTL ID : 1ru9.1

Crystal Structure (A) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 4.6 with a data set collected in-house.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.167, S.181, T.183 Chain B: F.172, P.173, T.182, L.183, S.184 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.167, A:S.181, A:T.183, A:T.183, B:P.173, B:S.184, B:S.184 Water bridges: B:T.182, B:T.182 GOL.4: 4 residues within 4Å: Chain A: T.102, F.103 Chain B: K.45, L.46 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:L.46, B:W.48 Hydrogen bonds: A:F.103, A:F.103 GOL.5: 3 residues within 4Å: Chain B: R.72, D.73, T.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.72, B:T.74, B:S.75 Water bridges: B:R.72 GOL.6: 3 residues within 4Å: Chain B: D.32, Y.54, W.101 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.32, B:D.32, B:Y.54 Water bridges: B:W.101 GOL.7: 6 residues within 4Å: Chain A: E.128 Chain B: S.126, V.127, Y.128, V.212, K.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.127, B:K.214

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: N.39, L.41, W.94, F.103 Chain B: L.99, W.109 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.99, B:W.109, A:W.94, A:F.103 Hydrogen bonds: B:W.109, A:N.39

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.3: 11 residues within 4Å: Chain A: F.37, W.94, G.96, Y.101 Chain B: A.34, N.36, Y.51, L.99, L.100, W.101, G.104 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.94 pi-Stacking: A:F.37, A:Y.101 Hydrogen bonds: B:N.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, X. et al., Probing the antibody-catalyzed water-oxidation pathway at atomic resolution. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-03-02

Peptides

immunoglobulin igg2a, light chain: A
immunoglobulin igg2a, heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

immunoglobulin igg2a, light chain

immunoglobulin igg2a, heavy chain

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