SMTL ID : 3fby.3 (2 other biounits)

The crystal structure of the signature domain of cartilage oligomeric matrix protein.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN-MAN.1: 10 residues within 4Å: Chain A: D.34, D.373, R.481, R.532, N.534, T.536, I.537, P.538, E.539 Ligands: SO4.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.539, A:E.539, A:E.539

29 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.61, D.63, D.65, F.67, D.82 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.61, A:D.63, A:D.65, A:F.67, A:D.82 CA.3: 8 residues within 4Å: Chain A: D.63, D.65, D.82, C.84, V.87, P.88, N.89, Q.92 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.65, A:D.82, A:D.82, A:C.84, A:V.87 CA.4: 8 residues within 4Å: Chain A: D.94, D.96, D.98, I.100, D.102, D.105, A.108 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.94, A:D.96, A:D.98, A:I.100, A:D.105 CA.5: 5 residues within 4Å: Chain A: D.96, D.98, D.105, D.107 Ligands: CA.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:D.105, A:D.105 CA.6: 6 residues within 4Å: Chain A: D.107, D.109, D.111, V.113, D.118 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.107, A:D.109, A:D.111, A:V.113, A:D.118 CA.7: 8 residues within 4Å: Chain A: D.109, D.111, D.118, C.120, V.123, R.124, N.125 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.109, A:D.111, A:D.118, A:C.120, A:V.123 CA.8: 7 residues within 4Å: Chain A: N.130, D.132, D.134, W.136, D.141, R.144 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.132, A:D.132, A:D.134, A:W.136, A:D.141 CA.9: 7 residues within 4Å: Chain A: D.132, D.134, D.141, C.143, Q.146, N.148 Ligands: CA.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.132, A:D.134, A:D.141, A:C.143, A:Q.146 CA.10: 8 residues within 4Å: Chain A: D.153, T.154, D.155, D.157, R.159, G.160, D.164, I.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.153, A:D.155, A:D.157, A:R.159 CA.11: 5 residues within 4Å: Chain A: D.155, D.157, D.164, D.166, G.169 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.155, A:D.164, A:D.166 CA.12: 6 residues within 4Å: Chain A: D.166, D.168, D.170, I.172, D.177 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.166, A:D.168, A:D.170, A:I.172, A:D.177 CA.13: 9 residues within 4Å: Chain A: D.168, D.170, D.177, C.179, P.180, V.182, P.183, N.184 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.168, A:D.177, A:D.177, A:C.179, A:V.182 CA.14: 6 residues within 4Å: Chain A: D.189, D.191, D.193, I.195, D.197, D.200 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.189, A:D.191, A:I.195, A:D.200 CA.15: 8 residues within 4Å: Chain A: D.191, D.193, D.200, C.202, K.205, S.206, N.207, Q.210 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.191, A:D.193, A:D.200, A:C.202, A:K.205 CA.16: 6 residues within 4Å: Chain A: D.212, D.214, D.216, F.217, V.218, D.223 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.212, A:D.214, A:D.216, A:V.218, A:D.223 CA.17: 4 residues within 4Å: Chain A: D.214, D.216, D.223, D.225 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.216, A:D.223, A:D.223, A:D.225 CA.18: 7 residues within 4Å: Chain A: D.227, D.229, D.231, H.233, D.235, D.238 Ligands: CA.19 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.227, A:D.229, A:D.231, A:H.233, A:D.238 CA.19: 8 residues within 4Å: Chain A: D.229, D.231, D.238, C.240, V.243, P.244, N.245 Ligands: CA.18 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.229, A:D.231, A:D.238, A:D.238, A:C.240 CA.20: 6 residues within 4Å: Chain A: D.250, D.252, D.254, Q.256, G.257, D.261 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.250, A:D.252, A:D.254, A:Q.256, A:D.261 CA.21: 5 residues within 4Å: Chain A: D.252, D.254, D.261, D.263, N.266 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.252, A:D.254, A:D.261, A:D.263 CA.22: 4 residues within 4Å: Chain A: D.258, D.261, D.264, D.271 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.258, A:D.261, A:D.264, A:D.271, H2O.1 CA.23: 6 residues within 4Å: Chain A: D.263, D.265, D.267, V.269, D.274 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.263, A:D.265, A:D.267, A:V.269, A:D.274 CA.24: 8 residues within 4Å: Chain A: D.265, D.267, D.274, C.276, V.279, P.280, N.281 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.265, A:D.267, A:D.274, A:C.276, A:V.279 CA.25: 7 residues within 4Å: Chain A: D.286, D.288, D.290, V.292, G.293, D.294, Q.297 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.286, A:D.290, A:V.292 CA.26: 5 residues within 4Å: Chain A: D.299, D.301, D.303, V.305, D.310 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.299, A:D.301, A:D.303, A:V.305, A:D.310 CA.27: 6 residues within 4Å: Chain A: D.301, D.303, D.310, C.312, N.315, V.318 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.301, A:D.303, A:D.310, A:C.312, A:V.318 CA.28: 4 residues within 4Å: Chain A: N.357, D.385, D.387, S.520 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.385, A:D.385, A:D.387, A:S.520, A:S.520 CA.29: 5 residues within 4Å: Chain A: V.383, T.384, D.385, Q.408, D.470 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.383, A:D.385, A:D.470, H2O.1 CA.30: 4 residues within 4Å: Chain A: D.385, D.386, D.387, Q.411 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.386, A:D.387

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

SO4.31: 2 residues within 4Å: Chain A: R.350, R.530 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.350, A:R.530 SO4.32: 1 residues within 4Å: Chain A: F.477 No protein-ligand interaction detected (PLIP) SO4.33: 5 residues within 4Å: Chain A: Q.479, P.538, E.539 Ligands: NAG-NAG-MAN-MAN-MAN.1, NAG-NAG-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.479, A:E.539

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, K. et al., The crystal structure of the signature domain of cartilage oligomeric matrix protein: implications for collagen, glycosaminoglycan and integrin binding. Faseb J. (2009)

Release Date

2009-06-23

Peptides

Cartilage oligomeric matrix protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Cartilage oligomeric matrix protein

Related Entries With Identical Sequence