SMTL ID : 5l9d.1

AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSYLATED, CRYSTAL FORM I, parsimonious model

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

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

PG4.1: 7 residues within 4Å: Chain A: G.44, L.45, E.46, K.63 Chain B: F.99, G.100, S.101 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:G.44, B:L.4, B:F.99, B:F.99 PG4.5: 6 residues within 4Å: Chain A: P.14, G.15, S.85, L.86, A.87, S.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.118 Water bridges: A:S.118

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.2: 7 residues within 4Å: Chain A: E.62, K.63, F.64, G.66, K.67, E.89, D.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.66 Water bridges: A:K.67

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 3 residues within 4Å: Chain A: Y.50, N.55, G.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.50

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

PEG.4: 3 residues within 4Å: Chain A: T.30, Y.54, K.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.54, A:K.74 PEG.7: 3 residues within 4Å: Chain A: Y.50, D.103 Chain B: Y.92 No protein-ligand interaction detected (PLIP) PEG.8: 6 residues within 4Å: Chain A: Q.39, G.42, Q.43 Chain B: Q.39, T.86, Y.88 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.39, A:G.42, A:Q.43, B:T.86, B:T.86, B:Y.88

1 x K: POTASSIUM ION(Non-covalent)

K.6: 1 residues within 4Å: Chain A: D.212 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.212, A:D.212, H2O.2

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

NAG.9: 1 residues within 4Å: Chain B: N.26 1 PLIP interactions: 1 interactions with chain B 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

2016-08-03

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

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