SMTL ID : 1hjv.1

Crystal structure of hcgp-39 in complex with chitin tetramer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

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

NAG-NAG-NAG.1: 3 residues within 4Å: Chain A: Y.13, E.49, W.50 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.3: 3 residues within 4Å: Chain B: Y.13, E.49, W.50 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.5: 3 residues within 4Å: Chain C: Y.13, E.49, W.50 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.7: 3 residues within 4Å: Chain D: Y.13, E.49, W.50 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG-NAG.2: 23 residues within 4Å: Chain A: Y.6, W.10, F.37, G.77, W.78, N.79, A.117, L.119, Y.120, A.156, G.160, T.163, M.183, Y.185, D.186, F.187, F.240, R.242, E.269, T.272, W.331, L.335 Ligands: SO4.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.240, A:T.272 Hydrogen bonds: A:W.78, A:N.79, A:N.79, A:E.269, A:E.269 Water bridges: A:R.14, A:R.14, A:G.77 NAG-NAG-NAG-NAG.4: 22 residues within 4Å: Chain B: Y.6, W.10, F.37, W.78, N.79, A.117, L.119, Y.120, A.156, G.160, T.163, M.183, Y.185, D.186, F.187, F.240, R.242, E.269, T.272, W.331, L.335 Ligands: SO4.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.240, B:T.272 Hydrogen bonds: B:W.78, B:N.79, B:N.79, B:E.269 Water bridges: B:G.77 NAG-NAG-NAG-NAG.6: 18 residues within 4Å: Chain C: Y.6, W.10, F.37, G.77, W.78, N.79, L.119, Y.120, S.158, G.160, M.183, Y.185, D.186, F.240, R.242, E.269, W.331, L.335 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:W.78, C:N.79, C:N.79, C:E.269, C:E.269 Water bridges: C:R.14 NAG-NAG-NAG-NAG.8: 21 residues within 4Å: Chain D: Y.6, W.10, F.37, G.77, W.78, N.79, A.117, L.119, Y.120, A.156, G.160, M.183, Y.185, D.186, F.187, F.240, R.242, E.269, W.331, L.335 Ligands: SO4.23 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.240 Hydrogen bonds: D:N.79, D:N.79, D:E.269 Water bridges: D:W.10, D:E.269, D:E.269

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

NAG.9: 5 residues within 4Å: Chain A: N.39, I.40, S.41, N.42, R.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.39, A:N.42, A:R.84 Water bridges: A:I.40 NAG.13: 5 residues within 4Å: Chain B: N.39, I.40, S.41, N.42, R.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.39, B:N.42, B:R.84 NAG.17: 5 residues within 4Å: Chain C: N.39, I.40, S.41, W.48, R.84 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.40, C:W.48 NAG.21: 5 residues within 4Å: Chain D: N.39, I.40, S.41, W.48, R.84 No protein-ligand interaction detected (PLIP)

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

SO4.10: 5 residues within 4Å: Chain A: R.212, Y.218 Chain B: R.212, Y.218 Ligands: SO4.22 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.218, B:R.225 Water bridges: B:K.161, B:K.161, A:R.212, A:R.212 Salt bridges: B:R.212, A:R.212 SO4.11: 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: 7 residues within 4Å: Chain A: D.186, F.187, H.188, G.189, W.191, R.192 Ligands: NAG-NAG-NAG-NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.187, A:G.189 Salt bridges: A:R.192 SO4.14: 4 residues within 4Å: Chain B: R.203, D.211, R.212 Chain D: R.212 7 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: B:R.212 Salt bridges: B:R.203, B:R.212, D:R.212 Water bridges: A:R.212, A:R.212, A:R.212 SO4.15: 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 SO4.16: 7 residues within 4Å: Chain B: F.187, H.188, G.189, W.191, R.192, S.214 Ligands: NAG-NAG-NAG-NAG.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.189, B:W.191, B:S.214 Salt bridges: B:R.192 SO4.18: 6 residues within 4Å: Chain A: R.212, F.213 Chain B: R.212 Chain C: R.203, E.206, R.212 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Water bridges: A:R.212 Salt bridges: A:R.212, C:R.203, C:R.212 SO4.19: 4 residues within 4Å: Chain B: E.206 Chain C: R.212, Y.218 Chain D: R.225 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:E.206 Salt bridges: C:R.212, D:R.225 SO4.20: 2 residues within 4Å: Chain C: R.96, K.100 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.96 Salt bridges: C:R.96, C:K.100 SO4.22: 7 residues within 4Å: Chain A: R.212 Chain B: R.212, F.213 Chain D: R.203, E.206, R.212 Ligands: SO4.10 8 PLIP interactions: 2 interactions with chain B, 5 interactions with chain D, 1 interactions with chain A Water bridges: B:K.161, D:P.210, D:R.212, D:R.212, A:R.212 Salt bridges: B:R.212, D:R.203, D:R.212 SO4.23: 7 residues within 4Å: Chain D: D.186, F.187, H.188, G.189, W.191, R.192 Ligands: NAG-NAG-NAG-NAG.8 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.189 Salt bridges: D:R.192 SO4.24: 2 residues within 4Å: Chain D: R.96, K.100 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.96 Salt bridges: D:R.96, D:K.100

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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