- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.45 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x GLY- ARG- GLY- ASP- SER- PRO: RGD PEPTIDE(Non-covalent)
- 1 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
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 14 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 7 residues within 4Å:- Chain A: T.150, I.154, Y.155, N.158, S.161, W.162
- Chain C: N.55
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.161
SO4.5: 4 residues within 4Å:- Chain A: R.276, R.279, R.281
- Ligands: NAG-NAG-BMA-MAN.2
4 PLIP interactions:4 interactions with chain A- Water bridges: A:R.279, A:R.279
- Salt bridges: A:R.279, A:R.281
SO4.6: 2 residues within 4Å:- Chain A: P.383, S.384
No protein-ligand interaction detected (PLIP)SO4.7: 4 residues within 4Å:- Chain A: T.296, D.297, H.304, N.372
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:T.296, A:D.297, A:N.372
- Salt bridges: A:H.304
SO4.8: 6 residues within 4Å:- Chain A: S.161, W.162, D.224, S.225, S.226
- Ligands: GLY-ARG-GLY-ASP-SER-PRO.1
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:W.162, A:D.224
- Water bridges: A:D.224, A:S.226
SO4.9: 3 residues within 4Å:- Chain A: R.400, S.401, R.402
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.401, A:S.401, A:R.402
- Salt bridges: A:R.400, A:R.402
SO4.10: 4 residues within 4Å:- Chain A: F.10, P.410, F.411, Q.444
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.444
SO4.11: 3 residues within 4Å:- Chain A: R.386, P.412, T.413
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:T.413
- Water bridges: A:R.386, A:R.386, A:T.413
- Salt bridges: A:R.386
SO4.12: 4 residues within 4Å:- Chain A: N.227, Y.230, R.276, R.279
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:N.227, A:R.279
- Water bridges: A:S.225, A:Y.230, A:R.276, A:R.279
- Salt bridges: A:R.276
SO4.17: 7 residues within 4Å:- Chain B: Q.82, Q.106, Y.110, S.243, R.352, G.420, F.421
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.243, B:G.420
- Water bridges: B:R.352
- Salt bridges: B:R.352
SO4.18: 3 residues within 4Å:- Chain B: G.276, S.277, D.278
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.277, B:S.277, B:S.277
SO4.19: 4 residues within 4Å:- Chain A: Y.353
- Chain B: N.269, D.270, L.294
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.269
- Water bridges: B:N.269
SO4.24: 3 residues within 4Å:- Chain D: S.30, S.67, G.68
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:G.68
- Water bridges: D:S.30, D:S.30
SO4.25: 7 residues within 4Å:- Chain D: Q.37, K.39, M.45, L.47, V.58, P.59, F.62
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Q.37
- Salt bridges: D:K.39
- 6 x CA: CALCIUM ION(Non-covalent)
CA.13: 6 residues within 4Å:- Chain A: E.243, D.245, D.247, T.250, T.251, E.252
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.245, A:D.247, A:T.250, A:E.252, A:E.252
CA.14: 6 residues within 4Å:- Chain A: D.297, N.299, D.301, R.303, D.305, L.332
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.297, A:D.301, A:R.303, A:D.305, H2O.10
CA.15: 8 residues within 4Å:- Chain A: D.365, L.366, D.367, D.369, Y.371, D.373, L.393, G.394
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.365, A:D.367, A:D.369, A:Y.371, A:D.373
CA.16: 7 residues within 4Å:- Chain A: D.426, I.427, D.428, N.430, Y.432, D.434, A.450
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.428, A:Y.432, A:D.434, A:D.434, H2O.14
CA.21: 6 residues within 4Å:- Chain B: S.123, M.124, D.126, D.127, M.335, D.336
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:S.123, B:D.127, B:M.335, H2O.15, H2O.15
CA.22: 5 residues within 4Å:- Chain B: D.158, N.215, D.217, P.219, E.220
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
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhu, J. et al., Complete Integrin Headpiece Opening in Eight Steps. J.Cell Biol. (2013)
- Release Date
- 2013-06-05
- Peptides
- INTEGRIN ALPHA-IIB: A
INTEGRIN BETA-3: B
10E5 FAB HEAVY CHAIN: C
10E5 FAB LIGHT CHAIN: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
HD
L
SMTL ID : 3zdy.1 (1 other biounit)
Integrin alphaIIB beta3 headpiece and RGD peptide complex
INTEGRIN ALPHA-IIB
INTEGRIN BETA-3
10E5 FAB HEAVY CHAIN
10E5 FAB LIGHT CHAIN
Related Entries With Identical Sequence
2vc2.1 | 2vdk.1 | 2vdl.1 | 2vdm.1 | 2vdn.1 | 2vdo.1 | 2vdp.1 | 2vdq.1 | 2vdr.1 | 3fcu.1 | 3fcu.2 | 3fcu.3 | 3nid.1 | 3nid.2 | 3nif.1 | 3nif.2 | 3nig.1 | 3nig.2 | 3t3m.1 | 3t3m.2 | 3t3p.1 | 3t3p.2 | 3zdx.1 | 3zdx.2 | 3zdy.2 | 3zdz.1 | 3zdz.2 | 3ze0.1 | 3ze0.2 | 3ze1.1 more...less...3ze1.2 | 3ze2.1 | 3ze2.2 | 4z7n.1 | 4z7n.2 | 4z7o.1 | 4z7o.2 | 4z7q.1 | 4z7q.2 | 5hdb.3 | 5hdb.4 | 7l8p.1 | 7l8p.2 | 7l8p.3 | 7tct.1 | 7tct.2 | 7td8.1 | 7td8.2 | 7tho.1 | 7tho.2 | 7tmz.1 | 7tmz.2 | 7tpd.1 | 7tpd.2 | 7u60.1 | 7u60.2 | 7u9f.1 | 7u9f.2 | 7u9v.1 | 7u9v.2 | 7ubr.1 | 7ubr.2 | 7ucy.1 | 7ucy.2 | 7udg.1 | 7udg.2 | 7udh.1 | 7udh.2 | 7ue0.1 | 7ue0.2 | 7ufh.1 | 7ufh.2 | 7uh8.1 | 7uh8.2 | 7uje.1 | 7uje.2 | 7ujk.1 | 7ujk.2 | 7uk9.1 | 7uk9.2 | 7uko.1 | 7uko.2 | 7ukp.1 | 7ukp.2 | 7ukt.1 | 7ukt.2