SMTL ID : 5buo.1

A receptor molecule

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

1 x SGN- IDS: 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose(Non-covalent)

SGN-IDS.1: 6 residues within 4Å: Chain A: R.118, P.119, R.120, H.121, N.124 Ligands: CA.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.120, A:H.121, A:N.124 Salt bridges: A:R.118

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.66 Ligands: ACT.12, SCN.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.66 ZN.3: 3 residues within 4Å: Chain A: H.34, M.38, E.75 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.34, A:E.75, H2O.2 ZN.4: 2 residues within 4Å: Chain A: H.146 Ligands: SCN.14 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.146 ZN.5: 3 residues within 4Å: Chain A: H.20, H.89, H.139 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.20, A:H.89, A:H.139, H2O.2 ZN.6: 3 residues within 4Å: Chain A: H.143, I.158 Ligands: SCN.15 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.143, H2O.1 ZN.7: 4 residues within 4Å: Chain A: E.94, D.136, H.165, I.169 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.136, A:D.136, A:H.165

1 x CA: CALCIUM ION(Non-functional Binders)

CA.8: 1 residues within 4Å: Ligands: SGN-IDS.1 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: A.58, D.59, A.62, H.66 Ligands: ACT.12, SO4.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.58, A:D.59 GOL.10: 3 residues within 4Å: Chain A: E.94, H.165, V.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.94 GOL.11: 3 residues within 4Å: Chain A: M.42, W.45, E.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.45

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 6 residues within 4Å: Chain A: D.59, A.62, V.63, H.66 Ligands: ZN.2, GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.62, A:V.63 Salt bridges: A:H.66

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.13: 2 residues within 4Å: Chain A: H.66 Ligands: ZN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.66 SCN.14: 5 residues within 4Å: Chain A: R.82, L.85, V.86, H.146 Ligands: ZN.4 No protein-ligand interaction detected (PLIP) SCN.15: 5 residues within 4Å: Chain A: I.158, Q.161, V.162, H.165 Ligands: ZN.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.161

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

SO4.16: 3 residues within 4Å: Chain A: Q.65, H.66 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.65 Salt bridges: A:H.66

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 3 residues within 4Å: Chain A: F.23, H.143, H.146 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miles, L.A., NULL. To Be Published

Release Date

2016-07-13

Peptides

Amyloid beta A4 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amyloid beta A4 protein