SMTL ID : 1u8c.1

A novel adaptation of the integrin PSI domain revealed from its crystal structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-mer

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: 6 residues within 4Å: Chain A: E.15, G.16, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, N.266 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.213, A:F.217 Hydrogen bonds: A:Q.214, A:Q.214, A:Q.214 NAG-NAG.3: 3 residues within 4Å: Chain A: F.558, E.560, N.585 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: D.751, N.950 No protein-ligand interaction detected (PLIP)

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

NAG-NDG.4: 1 residues within 4Å: Chain A: N.943 No protein-ligand interaction detected (PLIP) NAG-NDG.6: 4 residues within 4Å: Chain A: I.654 Chain B: Y.531, Y.557, N.559 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.531, A:I.654 NAG-NDG.7: 10 residues within 4Å: Chain A: P.758, L.838 Chain B: K.646, D.647, T.648, G.649, K.650, N.654, R.666, Q.668 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.646, B:G.649, B:N.654, B:R.666, B:K.650 Hydrophobic interactions: A:P.758

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

NAG.8: 2 residues within 4Å: Chain A: N.260, S.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.260, A:S.262, A:S.262 NAG.9: 3 residues within 4Å: Chain A: P.451, N.458, T.460 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.451 Hydrogen bonds: A:N.458, A:N.458 NAG.10: 4 residues within 4Å: Chain A: N.821, Q.885, V.886, G.887 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.821 NAG.16: 4 residues within 4Å: Chain A: R.248, M.272 Chain B: N.316, N.320 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.320 Hydrophobic interactions: A:R.248 NAG.17: 3 residues within 4Å: Chain B: N.371, S.398, E.400 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.398

6 x CA: CALCIUM ION(Non-covalent)

CA.11: 6 residues within 4Å: Chain A: D.230, N.232, D.234, G.235, I.236, D.238 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.230, A:I.236, A:D.238 CA.12: 6 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292, Q.320 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, A:D.292 CA.13: 6 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, N.356, D.357 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.349, A:D.351, A:D.353, A:F.355, A:D.357 CA.14: 6 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, P.420, D.421 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:P.420, A:D.421 CA.15: 5 residues within 4Å: Chain A: C.596, G.597, D.599, V.601, E.636 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.596, A:D.599, A:V.601, A:E.636, A:E.636 CA.18: 4 residues within 4Å: Chain B: S.123, D.126, D.127, M.335 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.123, B:D.126, B:D.127, B:M.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, J.P. et al., A novel adaptation of the integrin PSI domain revealed from its crystal structure. J.Biol.Chem. (2004)

Release Date

2004-12-28

Peptides

Integrin alpha-V: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-V

Integrin beta-3

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