SMTL ID : 7la4.1

Integrin AlphaIIbBeta3-PT25-2 Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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.1: 2 residues within 4Å: Chain D: N.125 Ligands: NAG-NAG-MAN.3 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.2: 7 residues within 4Å: Chain B: D.28 Chain C: E.260, R.312, M.316 Chain D: N.342, L.343, N.346 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.312, C:R.312

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.3: 6 residues within 4Å: Chain D: N.125, N.397, P.407, S.424, E.426 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain C: E.274, D.276, D.278, T.281, T.282, E.283 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.274, C:E.274, C:D.276, C:D.278, C:E.283 CA.5: 5 residues within 4Å: Chain C: D.328, N.330, D.332, R.334, D.336 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.328, C:D.332, C:R.334, C:D.336, H2O.1 CA.6: 6 residues within 4Å: Chain C: D.396, L.397, D.398, D.400, Y.402, D.404 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.396, C:D.398, C:Y.402, C:D.404, H2O.1 CA.7: 5 residues within 4Å: Chain C: D.457, D.459, N.461, Y.463, D.465 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.457, C:Y.463, C:D.465, C:D.465, H2O.1 CA.10: 5 residues within 4Å: Chain D: S.149, D.152, D.153, D.277, M.361 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:S.149, D:D.152, D:D.152 CA.11: 5 residues within 4Å: Chain D: D.184, N.241, D.243, P.245, E.246 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.184, D:D.243, D:P.245

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

NAG.8: 1 residues within 4Å: Chain C: N.46 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain D: S.147, S.149, E.246, D.277 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.147, D:E.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nesic, D. et al., Electron microscopy shows that binding of monoclonal antibody PT25-2 primes integrin alpha IIb beta 3 for ligand binding. Blood Adv (2021)

Release Date

2022-01-12

Peptides

PT25-2 heavy chain: A
PT25-2 light chain: B
Integrin alpha-IIb: C
Integrin beta-3: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
B

PT25-2 heavy chain

PT25-2 light chain

Integrin alpha-IIb

Integrin beta-3

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