SMTL ID : 6v09.1

Crystal structure of human recombinant Beta-2 glycoprotein I short tag (ST-B2GPI)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.246, W.247, S.248 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: H.184, N.186, W.187, T.188, K.189 Ligands: SO4.5 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.155 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.176, D.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.176

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

SO4.5: 3 residues within 4Å: Chain A: H.184 Ligands: NAG-NAG-BMA.2, SO4.6 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: Y.159, T.182, T.183 Ligands: SO4.5 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: T.105, G.106, F.107, Y.159 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: G.207, H.228 Ligands: SO4.9 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: D.205, N.206 Ligands: SO4.8 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: P.204, D.205, S.252, C.253 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: G.52, G.53, M.54 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain A: S.50, R.51, G.52 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: F.174, G.175, K.243 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: Y.219, K.220, K.243 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: V.49, R.75 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: P.23, F.24, K.45 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: M.54, R.55, K.56 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain A: D.334 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain A: R.89, Y.90, T.98, I.99, S.100 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: P.215, T.216, Y.218 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: G.226, C.227, S.232, L.233 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: G.235, P.236, E.237 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Chain A: K.274 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain A: R.160, D.161, T.162 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain A: C.227, H.228, D.229 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain A: E.321, S.323 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain A: T.183, H.184 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain A: V.49, R.75, V.76 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain A: Q.307 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain A: S.139, I.140, P.141, T.142, L.190 Ligand excluded by PLIP

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