SMTL ID : 6v06.1

Crystal structure of Beta-2 glycoprotein I purified from plasma (pB2GPI)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- MAN- MAN- NAG: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN-MAN-NAG.1: 1 residues within 4Å: Chain A: N.143 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- BMA- MAN- NAG: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-BMA-MAN-NAG.2: 3 residues within 4Å: Chain A: H.172, N.174, W.175 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- BMA- MAN: beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-BMA-MAN.3: 4 residues within 4Å: Chain A: L.232, N.234, W.235, S.236 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-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-BMA-NAG.4: 2 residues within 4Å: Chain A: N.164, D.165 No protein-ligand interaction detected (PLIP)

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: H.172 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.172 SO4.6: 4 residues within 4Å: Chain A: Y.147, T.170, T.171 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.147, A:T.171 Water bridges: A:R.148 SO4.7: 4 residues within 4Å: Chain A: T.93, G.94, F.95, L.146 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.121, A:I.121, A:Y.147 SO4.8: 6 residues within 4Å: Chain A: C.186, P.187, F.188, P.203, T.204, L.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.186, A:P.203, A:L.205 SO4.9: 4 residues within 4Å: Chain A: S.38, R.39, G.40, G.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.38, A:G.40 Salt bridges: A:R.39 SO4.10: 3 residues within 4Å: Chain A: F.162, G.163, K.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.163 Salt bridges: A:K.231 SO4.11: 2 residues within 4Å: Chain A: V.37, R.63 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.63, A:R.63 Salt bridges: A:R.63 SO4.12: 3 residues within 4Å: Chain A: P.11, F.12, K.33 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.12 Water bridges: A:D.9, A:K.33, A:K.33 Salt bridges: A:K.33 SO4.13: 3 residues within 4Å: Chain A: P.203, T.204, Y.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.204, A:Y.206, A:Y.206 Water bridges: A:K.185 SO4.14: 3 residues within 4Å: Chain A: R.43, K.44, F.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.44, A:K.44 Water bridges: A:R.43 SO4.15: 3 residues within 4Å: Chain A: V.37, R.63, V.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.64 Salt bridges: A:R.63 SO4.16: 7 residues within 4Å: Chain A: A.252, T.253, F.307, S.311, D.319, A.320, S.321 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.253, A:S.311, A:S.311, A:A.320, A:S.321, A:S.321, A:S.321 SO4.17: 3 residues within 4Å: Chain A: N.283, K.284, E.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.284, A:E.285

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.18: 5 residues within 4Å: Chain A: R.191, D.193, N.194, G.195, H.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.191, A:D.193, A:D.193 Water bridges: A:R.191 Salt bridges: A:H.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruben, E. et al., The J-elongated conformation of beta2-glycoprotein I predominates in solution: implications for our understanding of antiphospholipid syndrome. J.Biol.Chem. (2020)

Release Date

2020-06-17

Peptides

Beta-2-glycoprotein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-2-glycoprotein 1

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