SMTL ID : 8vs6.1

L-TGF-b3/avb8

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-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: 12 residues within 4Å: Chain B: T.212, A.213, Q.214, F.217, L.222, M.252, Y.254, Y.256, S.263, L.264, Y.265, N.266 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.213, B:F.217 Hydrogen bonds: B:Q.214, B:Q.214

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

NAG-NAG.2: 8 residues within 4Å: Chain B: E.15, G.16, S.17, K.42, A.43, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.191, T.193, E.194, K.197 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.193 NAG-NAG.4: 7 residues within 4Å: Chain C: E.90, N.92, M.94, I.364, R.370, N.389, T.391 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 11 residues within 4Å: Chain C: T.74, Q.75, L.100, Y.103, P.104, R.140, K.232, E.233, A.234, N.414, E.415 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.100

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

NAG.6: 6 residues within 4Å: Chain B: N.232, D.234, D.257, K.259, N.260, S.262 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.260 NAG.11: 4 residues within 4Å: Chain B: S.305 Chain C: Y.358, F.359, N.360 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.360 NAG.12: 2 residues within 4Å: Chain C: N.379, T.381 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.379

5 x CA: CALCIUM ION

CA.7: 6 residues within 4Å: Chain B: D.284, I.285, N.286, D.288, Y.290, D.292 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.284, B:D.288, B:Y.290, B:D.292, B:D.292 CA.8: 8 residues within 4Å: Chain B: D.349, L.350, D.351, D.353, F.355, D.357, N.377, G.378 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.349, B:D.351, B:D.353, B:F.355, B:D.357 CA.9: 6 residues within 4Å: Chain B: D.413, D.415, N.417, Y.419, D.421, A.437 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.413, B:D.415, B:Y.419, B:D.421 CA.10: 6 residues within 4Å: Chain B: D.230, F.231, N.232, D.234, I.236, D.238 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.230, B:D.234, B:I.236, B:D.238 CA.13: 7 residues within 4Å: Chain C: D.151, N.207, D.209, T.210, P.211, E.212, H.247 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.151, C:D.209, C:D.209, C:P.211

1 x MG: MAGNESIUM ION

MG.14: 7 residues within 4Å: Chain A: D.240 Chain C: D.112, S.114, S.116, E.212, D.243, Q.244 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:S.114, C:S.116, C:E.212, A:D.240

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-3 proprotein: A
Integrin alpha-V: B
Integrin beta-8: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
B

Transforming growth factor beta-3 proprotein

Integrin alpha-V

Integrin beta-8

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