SMTL ID : 1gr3.1

Structure of the human collagen X NC1 trimer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.1: 4 residues within 4Å: Chain A: W.91, Y.105, S.139 Chain C: Y.147 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:Y.147, C:Y.147, A:W.91, A:W.91, A:Y.105, A:Y.105 Hydrogen bonds: A:Y.105 CPS.5: 4 residues within 4Å: Chain A: Y.147 Chain B: W.91, Y.105, S.139 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.91, B:W.91, B:Y.105, B:Y.105, A:Y.147, A:Y.147 Hydrogen bonds: B:Y.105 CPS.9: 4 residues within 4Å: Chain B: Y.147 Chain C: W.91, Y.105, S.139 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:Y.147, B:Y.147, C:W.91, C:W.91, C:Y.105, C:Y.105 Hydrogen bonds: C:Y.105

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: D.114 Chain B: D.114 Chain C: D.114 Ligands: CA.4, CA.6, CA.8, CA.10, CA.12 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.114, A:D.114, B:D.114, H2O.1, H2O.4 CA.4: 8 residues within 4Å: Chain A: D.106, E.107, D.114 Chain C: L.113, D.114 Ligands: CA.2, CA.6, CA.10 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:D.106, A:E.107, A:D.114, C:L.113, C:D.114 CA.6: 8 residues within 4Å: Chain A: D.114 Chain B: D.114 Chain C: D.114 Ligands: CA.2, CA.4, CA.8, CA.10, CA.12 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.114, A:D.114, B:D.114, H2O.1, H2O.3 CA.8: 8 residues within 4Å: Chain A: L.113, D.114 Chain B: D.106, E.107, D.114 Ligands: CA.2, CA.6, CA.10 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:L.113, A:D.114, B:D.106, B:E.107, B:D.114 CA.10: 8 residues within 4Å: Chain A: D.114 Chain B: D.114 Chain C: D.114 Ligands: CA.2, CA.4, CA.6, CA.8, CA.12 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.114, A:D.114, B:D.114, H2O.3, H2O.4 CA.12: 8 residues within 4Å: Chain B: L.113, D.114 Chain C: D.106, E.107, D.114 Ligands: CA.2, CA.6, CA.10 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:L.113, B:D.114, C:D.106, C:E.107, C:D.114

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: Q.115 Chain B: Q.115 Chain C: Q.115 Ligands: NA.7, NA.11 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.115, B:Q.115, B:Q.115, C:Q.115 NA.7: 5 residues within 4Å: Chain A: Q.115 Chain B: Q.115 Chain C: Q.115 Ligands: NA.3, NA.11 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:Q.115, B:Q.115, C:Q.115, C:Q.115 NA.11: 5 residues within 4Å: Chain A: Q.115 Chain B: Q.115 Chain C: Q.115 Ligands: NA.3, NA.7 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.115, A:Q.115, B:Q.115, C:Q.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bogin, O. et al., Insight Into Schmid Metaphyseal Chondrodysplasia from the Crystal Structure of the Collagen X Nc1 Domain Trimer. Structure (2002)

Release Date

2002-02-14

Peptides

COLLAGEN X: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

COLLAGEN X