SMTL ID : 5l7x.1

Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 5 residues within 4Å: Chain A: K.63, K.67, S.85, E.89, D.90 No protein-ligand interaction detected (PLIP)

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

PEG.2: 4 residues within 4Å: Chain A: Y.50, N.55, G.57, S.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.50 PEG.3: 5 residues within 4Å: Chain A: I.33, Y.50, D.103 Chain B: Y.92, H.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.93 PEG.4: 7 residues within 4Å: Chain A: Y.95, Q.110, G.111, T.113 Chain B: G.42, S.43, S.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.95 Water bridges: A:Q.110

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 9 residues within 4Å: Chain A: G.44, L.45, E.46, K.63 Chain B: V.3, L.4, F.99, G.100, S.101 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:L.4, A:G.44

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 2 residues within 4Å: Chain B: V.3, N.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.3 Hydrogen bonds: B:N.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naschberger, A. et al., The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-07-13

Peptides

Mouse Antibody Fab Fragment, IgG1-kappa Heavy Chain: A
Mouse Antibody Fab Fragment, IgG1-kappa Light Chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Mouse Antibody Fab Fragment, IgG1-kappa Heavy Chain

Mouse Antibody Fab Fragment, IgG1-kappa Light Chain

Related Entries With Identical Sequence