SMTL ID : 5l88.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 2 residues within 4Å: Chain B: A.25, N.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.26

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

PG4.2: 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: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.4 Water bridges: B:L.4, B:F.99, A:G.44 PG4.3: 2 residues within 4Å: Chain A: P.41, G.42 No protein-ligand interaction detected (PLIP) PG4.4: 5 residues within 4Å: Chain A: S.31, N.99, Y.100, S.102, D.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.99, A:S.102 PG4.9: 5 residues within 4Å: Chain A: P.14, G.15, S.85, L.86, S.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.85, A:S.118 Water bridges: A:S.118, A:S.118

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

PE8.5: 8 residues within 4Å: Chain A: E.62, K.63, F.64, G.66, K.67, S.85, E.89, D.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.89 Water bridges: A:G.66

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

PGE.6: 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 PGE.12: 4 residues within 4Å: Chain A: V.93, Q.110, G.111 Chain B: G.42 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.113 PGE.14: 2 residues within 4Å: Chain B: T.198, K.200 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.200 PGE.15: 3 residues within 4Å: Chain B: N.32, Y.50, N.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.32, B:Y.50 PGE.16: 5 residues within 4Å: Chain A: R.218, D.219 Chain B: S.123, L.126, T.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.219 Water bridges: A:P.217, A:R.218

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

PEG.7: 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.8: 5 residues within 4Å: Chain A: S.88, S.91, L.114, T.115, Y.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88 PEG.10: 7 residues within 4Å: Chain A: Q.39, P.41, G.42, Q.43 Chain B: Q.39, T.86, Y.88 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.39, A:G.42, A:Q.43, B:T.86, B:T.86, B:Y.88 Water bridges: B:G.42

1 x K: POTASSIUM ION(Non-covalent)

K.11: 1 residues within 4Å: Chain A: D.212 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.212, A:D.212, H2O.3, H2O.5

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

1PE.13: 5 residues within 4Å: Chain A: I.33, D.103 Chain B: Y.33, Y.92, H.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.103

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

Anti-afamin antibody N14, Fab fragment, heavy chain: A
Anti-afamin antibody N14, Fab fragment, light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Anti-afamin antibody N14, Fab fragment, heavy chain

Anti-afamin antibody N14, Fab fragment, light chain

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