SMTL ID : 7u9f.2 (1 other biounit)

Integrin alpha IIB beta3 complex with BMS compound 4 in Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: R.281 Chain B: N.316, L.317, N.320 Ligands: SO4.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.281 Water bridges: A:S.261

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.2: 5 residues within 4Å: Chain B: N.371, S.398, I.399, E.400 Ligands: NAG.15 No protein-ligand interaction detected (PLIP)

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: A.89, R.90, H.112, K.124 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.112, A:K.124 SO4.4: 3 residues within 4Å: Chain A: R.400, S.401, R.402 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.400, A:S.401, A:S.401, A:R.402 Salt bridges: A:R.402 SO4.5: 4 residues within 4Å: Chain A: N.227, Y.230, R.276, R.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.227, A:Y.230 Salt bridges: A:R.276, A:R.279 SO4.11: 3 residues within 4Å: Chain A: R.279, R.281 Ligands: NAG-NAG-BMA-MAN.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.276 Salt bridges: A:R.279, A:R.281

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: Q.106 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.7: 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:E.243, A:D.245, A:D.247, A:T.250, A:E.252 CA.8: 5 residues within 4Å: Chain A: D.297, N.299, D.301, R.303, D.305 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.1 CA.9: 6 residues within 4Å: Chain A: D.365, L.366, D.367, D.369, Y.371, D.373 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.10: 5 residues within 4Å: Chain A: D.426, D.428, N.430, Y.432, D.434 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.426, A:D.428, A:Y.432, A:D.434, H2O.1

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.12: 3 residues within 4Å: Chain B: S.121, E.220 Ligands: I7R.17 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.121, B:E.220, H2O.8, H2O.10, H2O.10 MN.13: 5 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, M.335 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, B:M.335, H2O.12 MN.14: 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 NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.15: 4 residues within 4Å: Chain B: K.98, N.99, S.101 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.99

1 x I7R: (4-{[(5S)-3-{4-[(E)-imino(4-methylpiperazin-1-yl)methyl]phenyl}-4,5-dihydro-1,2-oxazol-5-yl]methyl}piperazin-1-yl)acetic acid(Non-covalent)

I7R.17: 18 residues within 4Å: Chain A: D.159, F.160, S.161, Y.189, Y.190, L.192, D.224, S.225, F.231 Chain B: S.121, Y.122, S.213, R.214, N.215, R.216, A.218, E.220 Ligands: MN.12 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.160, A:Y.190, A:Y.190, A:Y.190, A:Y.190, A:L.192 Hydrogen bonds: A:Y.189, B:Y.122, B:N.215, B:N.215 Salt bridges: A:D.224 pi-Stacking: A:F.231 Water bridges: B:S.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, F.Y. et al., A general chemical principle for creating closure-stabilizing integrin inhibitors. Cell (2022)

Release Date

2022-08-17

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

Integrin alpha-IIb

Integrin beta-3

Fab heavy chain

Fab light chain

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