SMTL ID : 3liz.1

crystal structure of bla g 2 complexed with Fab 4C3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 10 residues within 4Å: Chain A: N.277, I.278, S.279, Y.282, H.313, Y.314, R.329 Chain C: N.54, A.56, N.74 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.282, A:Y.282, A:R.329, A:R.329 Water bridges: C:N.54

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

NAG.2: 5 residues within 4Å: Chain A: A.153, V.155, N.319, E.321, N.322 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.153, A:V.155, A:E.321 Hydrogen bonds: A:N.319, A:E.321 Water bridges: A:E.321, A:N.322, A:N.322

3 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: H.313, E.332 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.313, A:E.332, H2O.1, H2O.2, H2O.5 CD.4: 1 residues within 4Å: Chain A: H.14 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.14, H2O.1, H2O.5, H2O.5 CD.5: 2 residues within 4Å: Chain A: E.144, E.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.144, A:E.148

7 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: Y.21, H.160, H.168, D.308, D.312 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.160, A:H.168, A:D.308, A:D.308, A:D.312 ZN.7: 3 residues within 4Å: Chain A: D.257, S.259 Chain B: E.93 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.93, A:D.257, A:S.259, H2O.5, H2O.16 ZN.8: 2 residues within 4Å: Chain A: E.92, D.106 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.106, H2O.5, H2O.12 ZN.9: 3 residues within 4Å: Chain A: K.198, D.302, H.303 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.303 ZN.10: 2 residues within 4Å: Chain A: C.298, H.300 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.298, A:H.300, H2O.9 ZN.17: 3 residues within 4Å: Chain A: K.260 Chain B: D.92, E.93 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.92, H2O.1, H2O.22, H2O.22, H2O.22 ZN.18: 2 residues within 4Å: Chain B: N.138 Chain C: H.170 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.170, H2O.16, H2O.29

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 3 residues within 4Å: Chain A: A.232, Y.233, D.302 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.232, A:Y.233, A:Y.233 EDO.12: 6 residues within 4Å: Chain A: R.162, Q.281, Y.282, I.284, Q.285, Q.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.162, A:Q.281, A:Q.286 Water bridges: A:Q.285 EDO.13: 5 residues within 4Å: Chain A: R.200, L.201, D.202, A.214, G.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.215 EDO.14: 3 residues within 4Å: Chain A: F.16, E.167, F.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.167 EDO.15: 2 residues within 4Å: Chain A: R.162, Y.282 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.281, A:Y.282 EDO.16: 3 residues within 4Å: Chain A: F.163, D.165, E.167 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glesner, J. et al., Mechanisms of allergen-antibody interaction of cockroach allergen Bla g 2 with monoclonal antibodies that inhibit IgE antibody binding. Plos One (2011)

Release Date

2010-12-15

Peptides

Aspartic protease Bla g 2: A
4C3 monoclonal antibody Light Chain: B
4C3 monoclonal antibody Heavy Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

Aspartic protease Bla g 2

4C3 monoclonal antibody Light Chain

4C3 monoclonal antibody Heavy Chain