SMTL ID : 7y1t.1

Complex of integrin alphaV/beta8 and L-TGF-beta1 at a ratio of 1:2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-NAG.1: 7 residues within 4Å: Chain B: Q.96, L.121, P.125, K.253, E.254, N.435, E.436 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.2: 2 residues within 4Å: Chain A: K.289, N.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: E.45, G.46, K.72, N.74 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-[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.4: 5 residues within 4Å: Chain A: Q.244, F.247, Y.284, Y.286, N.296 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.247 Hydrogen bonds: A:Q.244, A:Q.244, A:Y.286, A:Q.244

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

NAG.5: 2 residues within 4Å: Chain A: Q.525, N.555 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.525 NAG.10: 3 residues within 4Å: Chain B: N.113, N.410, T.412 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain B: N.212, T.214, E.215, K.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.212, B:T.214 NAG.12: 3 residues within 4Å: Chain B: Y.379, N.381, T.383 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain C: N.123, S.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.125

5 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.260, F.261, N.262, D.264, I.266, D.268 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.264, A:I.266, A:D.268, A:D.268 CA.7: 5 residues within 4Å: Chain A: D.314, N.316, D.318, Y.320, D.322 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.314, A:D.318, A:Y.320, A:D.322, A:D.322 CA.8: 6 residues within 4Å: Chain A: D.379, D.381, D.383, F.385, N.386, D.387 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.381, A:D.383, A:F.385, A:D.387, A:D.387 CA.9: 5 residues within 4Å: Chain A: D.444, D.446, N.448, Y.450, D.452 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.446, A:Y.450, A:D.452, A:D.452 CA.13: 5 residues within 4Å: Chain B: D.172, N.228, D.230, P.232, E.233 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.172, B:D.230, B:P.232, B:E.233

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

MN.14: 6 residues within 4Å: Chain B: D.133, S.135, S.137, E.233, Q.265 Chain C: D.233 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.135, B:S.137, C:D.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, Z. et al., Specificity of TGF-beta 1 signal designated by LRRC33 and integrin alpha V beta 8. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Integrin alpha-V: A
Integrin beta-8: B
Transforming growth factor beta-1 proprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Integrin alpha-V

Integrin beta-8

Transforming growth factor beta-1 proprotein

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