- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.00 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 6 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)
- 6 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
NAG-NAG-BMA.2: 5 residues within 4Å:- Chain A: G.233, D.234, D.257, K.259, N.260
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.6: 5 residues within 4Å:- Chain A: N.821, C.822, T.823, V.883, Q.885
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.12: 6 residues within 4Å:- Chain A: P.624, I.654
- Chain B: Y.531, Y.557, N.559, C.583
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:P.624, A:I.654
NAG-NAG-BMA.37: 5 residues within 4Å:- Chain C: G.233, D.234, D.257, K.259, N.260
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.41: 5 residues within 4Å:- Chain C: N.821, C.822, T.823, V.883, Q.885
No protein-ligand interaction detected (PLIP)NAG-NAG-BMA.47: 6 residues within 4Å:- Chain C: P.624, I.654
- Chain D: Y.531, Y.557, N.559, C.583
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:P.624, C:I.654
- 2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.3: 9 residues within 4Å:- Chain A: R.211, A.213, Q.214, A.215, F.217, Y.254, S.263, L.264, N.266
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Q.214, A:Q.214, A:Q.214
- Hydrophobic interactions: A:A.213, A:F.217
NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.38: 9 residues within 4Å:- Chain C: R.211, A.213, Q.214, A.215, F.217, Y.254, S.263, L.264, N.266
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:Q.214, C:Q.214, C:Q.214
- Hydrophobic interactions: C:A.213, C:F.217
- 2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
NAG-NAG-BMA-MAN.4: 8 residues within 4Å:- Chain A: E.448, Y.450, P.451, N.458, T.460, C.472, F.473, N.474
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.474, A:N.474
NAG-NAG-BMA-MAN.39: 8 residues within 4Å:- Chain C: E.448, Y.450, P.451, N.458, T.460, C.472, F.473, N.474
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.474, C:N.474
- 8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG-NAG.5: 4 residues within 4Å:- Chain A: E.560, P.583, A.584, N.585
No protein-ligand interaction detected (PLIP)NAG-NAG.8: 1 residues within 4Å:- Chain A: N.943
No protein-ligand interaction detected (PLIP)NAG-NAG.9: 3 residues within 4Å:- Chain B: N.99, F.100, S.101
No protein-ligand interaction detected (PLIP)NAG-NAG.10: 5 residues within 4Å:- Chain A: R.248
- Chain B: N.316, Q.319, N.320, E.323
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.843
NAG-NAG.40: 4 residues within 4Å:- Chain C: E.560, P.583, A.584, N.585
No protein-ligand interaction detected (PLIP)NAG-NAG.43: 1 residues within 4Å:- Chain C: N.943
No protein-ligand interaction detected (PLIP)NAG-NAG.44: 3 residues within 4Å:- Chain D: N.99, F.100, S.101
No protein-ligand interaction detected (PLIP)NAG-NAG.45: 5 residues within 4Å:- Chain C: R.248
- Chain D: N.316, Q.319, N.320, E.323
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:K.843
- 2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-NAG-BMA-MAN-MAN-MAN.7: 22 residues within 4Å:- Chain A: K.843, N.844, T.846, V.847
- Chain B: T.328, T.329, G.349, K.350, S.353, K.354, M.387, L.389, S.570, N.571, K.611, R.636, D.637, E.638, Y.669, E.671, K.676, S.677
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:S.353, B:T.328, B:K.350
- Hydrophobic interactions: B:R.636
NAG-NAG-BMA-MAN-MAN-MAN.42: 22 residues within 4Å:- Chain C: K.843, N.844, T.846, V.847
- Chain D: T.328, T.329, G.349, K.350, S.353, K.354, M.387, L.389, S.570, N.571, K.611, R.636, D.637, E.638, Y.669, E.671, K.676, S.677
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:S.353, D:T.328, D:K.350
- Hydrophobic interactions: D:R.636
- 12 x CA: CALCIUM ION(Non-covalent)
CA.14: 5 residues within 4Å:- Chain A: D.230, N.232, D.234, I.236, D.238
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.230, A:D.234, A:I.236, A:D.238, H2O.2
CA.15: 5 residues within 4Å:- Chain A: D.284, N.286, D.288, Y.290, D.292
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.16: 6 residues within 4Å:- Chain A: D.349, L.350, D.351, D.353, F.355, 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.17: 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:D.421, A:D.421
CA.18: 5 residues within 4Å:- Chain A: C.596, D.599, V.601, C.602, E.636
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.599, A:D.599, A:V.601, A:E.636, A:E.636
CA.29: 8 residues within 4Å:- Chain B: D.158, N.215, R.216, D.217, A.218, P.219, E.220, H.255
5 PLIP interactions:5 interactions with chain B- Metal complexes: B:D.158, B:D.217, B:D.217, B:P.219, B:E.220
CA.49: 5 residues within 4Å:- Chain C: D.230, N.232, D.234, I.236, D.238
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.230, C:D.234, C:I.236, C:D.238, H2O.6
CA.50: 5 residues within 4Å:- Chain C: D.284, N.286, D.288, Y.290, D.292
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.284, C:D.288, C:Y.290, C:D.292, C:D.292
CA.51: 6 residues within 4Å:- Chain C: D.349, L.350, D.351, D.353, F.355, D.357
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.349, C:D.351, C:D.353, C:F.355, C:D.357
CA.52: 6 residues within 4Å:- Chain C: D.413, D.415, N.417, Y.419, P.420, D.421
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.413, C:D.415, C:Y.419, C:D.421, C:D.421
CA.53: 5 residues within 4Å:- Chain C: C.596, D.599, V.601, C.602, E.636
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.599, C:D.599, C:V.601, C:E.636, C:E.636
CA.64: 8 residues within 4Å:- Chain D: D.158, N.215, R.216, D.217, A.218, P.219, E.220, H.255
5 PLIP interactions:5 interactions with chain D- Metal complexes: D:D.158, D:D.217, D:D.217, D:P.219, D:E.220
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.19: 3 residues within 4Å:- Chain A: Q.494, S.522, N.524
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.494, A:Q.494, A:S.522
NAG.20: 4 residues within 4Å:- Chain A: H.752, I.869, S.919, N.950
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.919, A:N.950
NAG.54: 3 residues within 4Å:- Chain C: Q.494, S.522, N.524
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Q.494, C:Q.494, C:S.522
NAG.55: 4 residues within 4Å:- Chain C: H.752, I.869, S.919, N.950
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:S.919, C:N.950
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.21: 4 residues within 4Å:- Chain A: S.516, S.520, H.521, S.522
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.516, A:S.522, A:S.522
- Salt bridges: A:H.521
SO4.22: 6 residues within 4Å:- Chain A: G.49, N.77, F.88, K.89, S.90, R.122
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:N.77, A:K.89, A:S.90, A:S.90
- Water bridges: A:R.122, A:R.122
- Salt bridges: A:R.122
SO4.23: 3 residues within 4Å:- Chain A: G.304, S.305, Q.310
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.305, A:Q.310
SO4.30: 8 residues within 4Å:- Chain B: S.70, D.71, K.72, S.78
- Chain D: K.619, I.639, E.640, S.641
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:D.71, B:K.72, B:S.78, D:S.641
- Salt bridges: D:K.619
SO4.31: 5 residues within 4Å:- Chain A: R.665
- Chain B: I.4, T.7, R.8, E.522
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:T.7
- Salt bridges: B:R.8, A:R.665
SO4.32: 4 residues within 4Å:- Chain B: V.359, R.360, D.361, L.362
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.361, B:L.362
SO4.56: 4 residues within 4Å:- Chain C: S.516, S.520, H.521, S.522
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:S.516, C:S.522, C:S.522
- Salt bridges: C:H.521
SO4.57: 6 residues within 4Å:- Chain C: G.49, N.77, F.88, K.89, S.90, R.122
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:N.77, C:K.89, C:S.90, C:S.90
- Water bridges: C:R.122, C:R.122
- Salt bridges: C:R.122
SO4.58: 3 residues within 4Å:- Chain C: G.304, S.305, Q.310
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:S.305, C:Q.310
SO4.65: 8 residues within 4Å:- Chain B: K.619, I.639, E.640, S.641
- Chain D: S.70, D.71, K.72, S.78
6 PLIP interactions:2 interactions with chain B, 4 interactions with chain D- Hydrogen bonds: B:S.641, D:D.71, D:D.71, D:K.72, D:S.78
- Salt bridges: B:K.619
SO4.66: 5 residues within 4Å:- Chain C: R.665
- Chain D: I.4, T.7, R.8, E.522
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain D- Salt bridges: C:R.665, D:R.8
- Hydrogen bonds: D:E.522
SO4.67: 4 residues within 4Å:- Chain D: V.359, R.360, D.361, L.362
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:D.361, D:L.362
- 14 x CL: CHLORIDE ION(Non-functional Binders)
CL.24: 1 residues within 4Å:- Chain B: R.563
Ligand excluded by PLIPCL.25: 2 residues within 4Å:- Chain A: E.270, K.330
Ligand excluded by PLIPCL.26: 2 residues within 4Å:- Chain A: R.99, S.100
Ligand excluded by PLIPCL.27: 1 residues within 4Å:- Chain A: R.888
Ligand excluded by PLIPCL.33: 1 residues within 4Å:- Chain B: M.535
Ligand excluded by PLIPCL.34: 1 residues within 4Å:- Chain B: Y.556
Ligand excluded by PLIPCL.35: 2 residues within 4Å:- Chain B: K.402, G.555
Ligand excluded by PLIPCL.59: 1 residues within 4Å:- Chain D: R.563
Ligand excluded by PLIPCL.60: 2 residues within 4Å:- Chain C: E.270, K.330
Ligand excluded by PLIPCL.61: 2 residues within 4Å:- Chain C: R.99, S.100
Ligand excluded by PLIPCL.62: 1 residues within 4Å:- Chain C: R.888
Ligand excluded by PLIPCL.68: 1 residues within 4Å:- Chain D: M.535
Ligand excluded by PLIPCL.69: 1 residues within 4Å:- Chain D: Y.556
Ligand excluded by PLIPCL.70: 2 residues within 4Å:- Chain D: K.402, G.555
Ligand excluded by PLIP- 2 x NI: NICKEL (II) ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dong, X. et al., AlphaV Beta3 Integrin Crystal Structures and their Functional Implications. Biochemistry (2012)
- Release Date
- 2012-12-12
- Peptides
- Integrin alpha-V: AC
Integrin beta-3: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AB
BD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.00 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 6 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)
- 6 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
- 2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
- 2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)
- 8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 12 x CA: CALCIUM ION(Non-covalent)
- 4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 14 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x NI: NICKEL (II) ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Dong, X. et al., AlphaV Beta3 Integrin Crystal Structures and their Functional Implications. Biochemistry (2012)
- Release Date
- 2012-12-12
- Peptides
- Integrin alpha-V: AC
Integrin beta-3: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AB
BD
B