SMTL ID : 8gcd.1

Full length Integrin AlphaIIbBeta3 in inactive state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(1-3)-[beta-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

NAG-NAG-BMA-MAN-BMA.1: 5 residues within 4Å: Chain A: W.293, R.312, R.931 Chain B: N.342, N.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.931, A:R.312

1 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

NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: S.395, N.397, S.424, I.425, E.426 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 5 residues within 4Å: Chain A: R.692 Chain B: Y.557, Y.583, N.585, C.609 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.692 NAG-NAG.4: 2 residues within 4Å: Chain B: K.124, N.125 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.124, B:K.124

7 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: E.274, D.276, D.278, T.281, T.282, E.283 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.274, A:D.276, A:D.278, A:T.281, A:E.283 CA.6: 5 residues within 4Å: Chain A: D.328, N.330, D.332, R.334, D.336 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.328, A:D.332, A:R.334, A:D.336, A:D.336 CA.7: 5 residues within 4Å: Chain A: D.396, D.398, D.400, Y.402, D.404 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.398, A:D.400, A:Y.402, A:D.404, A:D.404 CA.8: 6 residues within 4Å: Chain A: D.457, I.458, D.459, N.461, Y.463, D.465 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.457, A:D.459, A:Y.463, A:D.465, A:D.465 CA.9: 6 residues within 4Å: Chain A: C.633, G.634, E.635, D.636, D.637, E.673 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.633, A:D.636, A:E.673 CA.14: 5 residues within 4Å: Chain B: S.149, M.150, D.152, D.277, M.361 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.149, B:D.152, B:D.152 CA.15: 4 residues within 4Å: Chain B: D.184, N.241, D.243, P.245 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.184, B:D.243, B:D.243, B:P.245

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

NAG.10: 1 residues within 4Å: Chain A: N.46 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain A: N.601 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: D.278, N.280 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 3 residues within 4Å: Chain B: S.147, S.149, E.246 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.149, B:E.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, T. et al., Full-length alpha IIb beta 3 cryo-EM structure reveals intact integrin initiate-activation intrinsic architecture. Structure (2024)

Release Date

2024-03-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Integrin alpha-IIb

Integrin beta-3

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