SMTL ID : 1hjx.1

Ligand-induced signalling and conformational change of the 39 kD glycoprotein from human articular chondrocytes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.39, I.40, S.41, W.48, R.84 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain B: N.39, I.40, S.41, W.48, R.84 Ligands: GOL.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: N.39, I.40, S.41, W.48, R.84 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain D: N.39, I.40, S.41, T.47, W.48, R.84 No protein-ligand interaction detected (PLIP)

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

SO4.5: 2 residues within 4Å: Chain A: R.96, K.100 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.96, A:K.100 SO4.12: 5 residues within 4Å: Chain A: R.212 Chain B: R.203, D.211, R.212 Chain D: R.212 11 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: B:R.212, A:R.212 Water bridges: B:R.203, B:R.203, B:R.203, B:R.203, D:R.212, D:R.212 Salt bridges: B:R.203, B:R.212, D:R.212 SO4.13: 7 residues within 4Å: Chain A: K.161, R.212, Y.218 Chain B: K.161, R.212, Y.218, Y.222 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.218, B:Y.218 Water bridges: B:K.161, B:K.161, B:R.212, A:K.161 Salt bridges: B:K.161, B:R.212, A:K.161, A:R.212 SO4.14: 2 residues within 4Å: Chain B: R.96, K.100 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.96, B:K.100 SO4.15: 4 residues within 4Å: Chain B: K.161, R.212 Chain D: R.203, R.212 13 PLIP interactions: 4 interactions with chain B, 5 interactions with chain D, 4 interactions with chain A Water bridges: B:K.161, B:R.212, D:R.203, D:R.212, D:R.212, A:R.203, A:R.203, A:R.212 Salt bridges: B:K.161, B:R.212, D:R.203, D:R.212 Hydrogen bonds: A:R.212 SO4.18: 6 residues within 4Å: Chain A: R.212 Chain B: R.203, R.212 Chain C: R.203, R.212 Ligands: GOL.10 9 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:R.212, B:R.203 Water bridges: C:R.203, C:R.212, C:R.212, A:R.212 Salt bridges: C:R.203, C:R.212, A:R.212 SO4.19: 5 residues within 4Å: Chain B: E.206 Chain C: R.212, Y.218, R.225 Chain D: R.225 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 1 interactions with chain D Water bridges: C:K.161, C:R.225 Salt bridges: C:R.212, C:R.225, D:R.225 Hydrogen bonds: B:E.206 SO4.20: 2 residues within 4Å: Chain C: R.96, K.100 4 PLIP interactions: 4 interactions with chain C Water bridges: C:K.100, C:K.100 Salt bridges: C:R.96, C:K.100

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: Y.120, S.158, A.159, G.160, M.183, Y.185, D.186, F.187 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: W.78, Y.185, D.186, F.240, R.242, T.272, W.331 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: Y.218, G.221, Y.222, R.225 Chain B: Y.222 Chain D: E.206, D.207 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: K.126, Y.168, D.169, I.170, L.226 Chain B: L.224, R.225, G.227 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: R.203, P.210, D.211, R.212 Chain C: R.212 Ligands: SO4.18 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain A: G.189, G.196, H.197, P.200, R.203, S.209, S.214, Q.293 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: W.78, Y.185, D.186, F.240, R.242, T.272, W.331 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: S.41, N.42 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain C: Y.120, S.158, A.159, G.160, M.183, Y.185, D.186, F.187 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: F.202, Y.319 Chain C: Q.205, I.290, L.291, G.292 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain C: G.160, K.161, V.162, T.163 Ligand excluded by PLIP GOL.24: 3 residues within 4Å: Chain C: D.186, H.188, R.242 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain C: R.123, R.124, K.126, Q.127 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain D: Y.120, S.158, A.159, G.160, M.183, Y.185, D.186, F.187 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain D: G.189, H.197, P.200, R.203, S.209, S.214, V.253, Q.293 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain D: F.187, H.188, G.189, A.190, G.196, H.197, H.198, F.244 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Houston, D.R. et al., Structure and Ligand-Induced Conformational Change of the 39-kDa Glycoprotein from Human Articular Chondrocytes. J.Biol.Chem. (2003)

Release Date

2003-03-11

Peptides

CHITINASE-3 LIKE PROTEIN 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CHITINASE-3 LIKE PROTEIN 1

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