SMTL ID : 8vsd.1

avb8/L-TGF-b1/GARP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

hetero-1-1-1-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-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-MAN-MAN.1: 7 residues within 4Å: Chain B: A.213, Q.214, F.217, Y.254, S.263, L.264, N.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.214, B:Q.214 Hydrophobic interactions: B:F.217

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

NAG-NAG.2: 6 residues within 4Å: Chain B: E.15, G.16, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.120, T.122, E.123, K.126 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: N.21, I.293, R.299, N.318, V.319, T.320 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: L.29, K.161, E.162, N.343 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.29 Hydrogen bonds: C:E.162

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.6: 3 residues within 4Å: Chain B: D.257, N.260, S.262 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.260, B:S.262, B:S.262 NAG.11: 1 residues within 4Å: Chain C: N.289 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.289 NAG.12: 1 residues within 4Å: Chain C: N.308 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.308

5 x CA: CALCIUM ION

CA.7: 5 residues within 4Å: Chain B: D.284, N.286, D.288, Y.290, D.292 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.288, B:Y.290, B:D.292, B:D.292 CA.8: 4 residues within 4Å: Chain B: D.349, D.351, F.355, D.357 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.349, B:D.351, B:F.355, B:D.357, B:D.357 CA.9: 5 residues within 4Å: Chain B: D.415, N.417, Y.419, D.421, A.437 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.421, B:D.421 CA.10: 5 residues within 4Å: Chain B: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.234, B:D.234, B:I.236, B:D.238, B:D.238 CA.13: 5 residues within 4Å: Chain C: D.80, N.136, D.138, P.140, E.141 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.80, C:D.138, C:P.140

1 x MG: MAGNESIUM ION

MG.14: 4 residues within 4Å: Chain C: S.43, S.45, E.141 Chain D: D.217 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:S.45, C:E.141, C:E.141, D:D.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jin, M. et al., Dynamic allostery drives autocrine and paracrine TGF-beta signaling. Cell (2024)

Release Date

2024-09-11

Peptides

Transforming growth factor beta activator LRRC32: A
Integrin alpha-V heavy chain: B
Integrin beta-8: C
Transforming growth factor beta-1 proprotein: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
A

C
B

D
E

E
F

Transforming growth factor beta activator LRRC32

Integrin alpha-V heavy chain

Integrin beta-8

Transforming growth factor beta-1 proprotein

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