SMTL ID : 1yo8.1

Structure of the C-terminal domain of human thrombospondin-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

NAG-NAG-MAN.1: 3 residues within 4Å: Chain A: L.142, V.159, N.163 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 5 residues within 4Å: Chain A: D.319, R.489, N.522, T.524, T.597 No protein-ligand interaction detected (PLIP)

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

NAG.3: 5 residues within 4Å: Chain A: G.5, S.8, P.10, G.23, W.25 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: N.37, T.39, H.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.37

30 x CA: CALCIUM ION(Non-covalent)

CA.5: 7 residues within 4Å: Chain A: D.390, D.392, D.399, C.401, N.404, I.407, S.408 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.390, A:D.392, A:D.399, A:N.404, A:I.407 CA.6: 5 residues within 4Å: Chain A: D.388, D.390, D.392, I.394, D.399 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.388, A:D.390, A:D.392, A:I.394, A:D.399 CA.7: 5 residues within 4Å: Chain A: D.375, D.377, D.379, R.381, D.383 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.375, A:D.377, A:D.379, A:R.381, A:D.383 CA.8: 5 residues within 4Å: Chain A: D.352, D.354, D.356, V.358, D.363 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.352, A:D.354, A:D.356, A:V.358, A:D.363, H2O.3 CA.9: 7 residues within 4Å: Chain A: D.354, D.356, D.363, C.365, V.368, N.370, Q.373 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.354, A:D.356, A:D.363, A:C.365, A:V.368 CA.10: 6 residues within 4Å: Chain A: D.341, D.343, D.350, D.352, N.355 Ligands: CA.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.341, A:D.343, A:D.350, A:D.352, H2O.1 CA.11: 6 residues within 4Å: Chain A: D.339, D.341, D.343, Q.345, D.350 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.339, A:D.341, A:D.343, A:Q.345, A:D.350 CA.12: 4 residues within 4Å: Chain A: D.347, D.350, D.353, D.360 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.347, A:D.350, A:D.360, H2O.1, H2O.2 CA.13: 7 residues within 4Å: Chain A: D.318, D.320, D.327, C.329, I.332, S.333, N.334 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.318, A:D.320, A:D.327, A:C.329, A:I.332 CA.14: 5 residues within 4Å: Chain A: D.316, D.318, D.320, H.322, D.327 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.316, A:D.318, A:D.320, A:H.322, A:D.327, H2O.5 CA.15: 4 residues within 4Å: Chain A: D.303, D.305, D.312, N.314 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.303, A:D.305, A:D.312, A:D.312, H2O.5 CA.16: 5 residues within 4Å: Chain A: D.301, D.303, D.305, V.307, D.312 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.301, A:D.303, A:D.305, A:V.307, A:D.312, H2O.4 CA.17: 4 residues within 4Å: Chain A: N.446, D.474, D.476, S.609 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.474, A:D.476, A:S.609, A:S.609, H2O.3 CA.18: 4 residues within 4Å: Chain A: D.472, D.474, Q.497, D.559 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.472, A:D.474, A:D.559, H2O.1, H2O.4 CA.19: 4 residues within 4Å: Chain A: D.474, D.475, D.476, Q.500 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.475, A:D.476, A:D.476, H2O.2, H2O.4 CA.20: 5 residues within 4Å: Chain A: D.242, D.244, N.246, E.248, I.256 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.242, A:D.244, A:E.248, H2O.4 CA.21: 7 residues within 4Å: Chain A: D.280, D.282, D.289, C.291, V.294, N.296 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.280, A:D.282, A:D.289, A:C.291, A:V.294 CA.22: 6 residues within 4Å: Chain A: D.278, D.280, D.282, V.284, D.289 Ligands: CA.21 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.278, A:D.280, A:D.282, A:V.284, A:D.289, H2O.2 CA.23: 7 residues within 4Å: Chain A: D.257, D.259, D.266, C.268, V.271, N.273 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.257, A:D.259, A:D.266, A:C.268, A:V.271 CA.24: 6 residues within 4Å: Chain A: D.255, D.257, D.259, V.261, D.266 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.255, A:D.257, A:D.259, A:V.261, A:D.266 CA.25: 7 residues within 4Å: Chain A: D.221, D.223, D.230, C.232, V.235, N.237 Ligands: CA.26 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.223, A:D.230, A:D.230, A:C.232, A:V.235 CA.26: 6 residues within 4Å: Chain A: D.219, D.221, D.223, V.225, D.230 Ligands: CA.25 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.219, A:D.223, A:V.225, A:D.230, H2O.4 CA.27: 7 residues within 4Å: Chain A: D.198, D.200, D.207, C.209, L.212, N.214 Ligands: CA.28 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.198, A:D.200, A:D.207, A:C.209, A:L.212 CA.28: 6 residues within 4Å: Chain A: D.196, D.198, D.200, V.202, D.207 Ligands: CA.27 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.196, A:D.198, A:D.200, A:V.202, A:D.207, H2O.5 CA.29: 6 residues within 4Å: Chain A: D.183, D.185, D.187, I.189, D.194 Ligands: CA.30 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.183, A:D.185, A:D.187, A:D.194, H2O.4 CA.30: 6 residues within 4Å: Chain A: D.185, D.187, D.194, D.196, N.199 Ligands: CA.29 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.185, A:D.187, A:D.194, A:D.196, H2O.4 CA.31: 4 residues within 4Å: Chain A: D.191, D.194, D.197, D.204 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.191, A:D.197, A:D.204, H2O.3, H2O.3 CA.32: 5 residues within 4Å: Chain A: D.147, D.149, D.151, W.153, D.171 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.147, A:D.149, A:D.151, A:W.153, A:D.171, H2O.1 CA.33: 7 residues within 4Å: Chain A: D.149, D.151, D.171, C.173, L.176, P.177, N.178 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.149, A:D.151, A:D.171, A:C.173, A:L.176 CA.34: 6 residues within 4Å: Chain A: D.43, L.44, E.46, N.65, T.66, G.69 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.43, A:L.44, A:E.46, A:T.66, A:G.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carlson, C.B. et al., Structure of the calcium-rich signature domain of human thrombospondin-2. Nat.Struct.Mol.Biol. (2005)

Release Date

2005-09-27

Peptides

thrombospondin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

thrombospondin-2