SMTL ID : 1rul.1

Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: N.39, L.41, W.94 Chain B: L.99, W.109 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.94, B:L.99 Hydrogen bonds: A:N.39, B:W.109

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: L.165, S.167, S.181, S.182, T.183 Chain B: L.147, F.172, P.173, T.182, L.183, S.184 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.181, A:T.183, A:T.183, B:P.173, B:S.184 Water bridges: B:K.149, B:K.149 GOL.4: 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 Water bridges: B:R.72, B:R.72 GOL.5: 4 residues within 4Å: Chain B: D.32, Y.54, W.101, Y.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.32, B:D.32 Water bridges: B:Y.102 GOL.6: 6 residues within 4Å: Chain A: E.128 Chain B: S.126, V.127, Y.128, V.212, K.214 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.127, B:K.214, A:E.128

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.3: 10 residues within 4Å: Chain A: W.94, G.96, Y.101 Chain B: A.34, N.36, W.48, Y.51, L.99, L.100, 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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