SMTL ID : 5ffo.1

Integrin alpha V beta 6 in complex with pro-TGF-beta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.49 Å

Oligo State

hetero-2-2-4-mer

Ligands

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

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: E.15, G.16, K.42, N.44, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain E: E.15, G.16, K.42, N.44, E.52 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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.2: 12 residues within 4Å: Chain A: F.231, N.232, D.257, K.259, N.260, Y.265, A.322, G.324 Chain H: K.136, V.137, P.162, D.164 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain H Hydrophobic interactions: A:N.232 Hydrogen bonds: H:K.136, H:K.136, H:D.164 NAG-NAG-BMA-MAN-MAN-MAN.9: 8 residues within 4Å: Chain E: F.231, N.232, D.257, K.259, N.260, Y.265, A.322, G.324 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:N.232

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN.3: 11 residues within 4Å: Chain A: T.212, A.213, Q.214, F.217, M.252, Y.254, Y.256, S.263, L.264, N.266 Chain E: K.82 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Q.214, A:Q.214, A:Y.256, E:K.82 NAG-NAG-BMA-MAN-MAN-MAN-MAN.10: 10 residues within 4Å: Chain E: T.212, A.213, Q.214, F.217, M.252, Y.254, Y.256, S.263, L.264, N.266 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.214, E:Q.214

2 x NAG- NAG- BMA- MAN: 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.4: 9 residues within 4Å: Chain A: Y.451, P.452, I.454, N.459, T.461, C.473, F.474, N.475, E.538 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.475, A:E.538 NAG-NAG-BMA-MAN.11: 8 residues within 4Å: Chain E: P.452, I.454, N.459, T.461, C.473, F.474, N.475, E.538 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.475, E:E.538

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.5: 4 residues within 4Å: Chain A: K.502, F.559, A.585, N.586 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: K.502, F.559, A.585, N.586 No protein-ligand interaction detected (PLIP)

3 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.6: 3 residues within 4Å: Chain C: E.48, N.55, R.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 5 residues within 4Å: Chain B: A.67, Y.75, F.76 Chain D: N.55, R.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 2 residues within 4Å: Chain G: N.55, R.58 No protein-ligand interaction detected (PLIP)

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.14: 5 residues within 4Å: Chain F: Y.75, F.76 Chain H: L.51, N.55, R.58 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.15: 5 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, A:D.292 CA.16: 6 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357, N.377 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.349, A:D.351, A:F.355, A:D.357, A:D.357 CA.17: 5 residues within 4Å: Chain A: D.414, D.416, N.418, Y.420, D.422 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.414, A:D.416, A:Y.420, A:D.422, A:D.422 CA.18: 5 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.230, A:D.234, A:I.236, A:D.238, A:D.238 CA.24: 5 residues within 4Å: Chain E: D.284, N.286, D.288, Y.290, D.292 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.284, E:D.288, E:Y.290, E:D.292, E:D.292 CA.25: 6 residues within 4Å: Chain E: D.349, D.351, D.353, F.355, D.357, N.377 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.349, E:D.351, E:F.355, E:D.357, E:D.357 CA.26: 5 residues within 4Å: Chain E: D.414, D.416, N.418, Y.420, D.422 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.414, E:D.416, E:Y.420, E:D.422, E:D.422 CA.27: 6 residues within 4Å: Chain E: D.230, N.232, D.234, I.236, D.238, D.257 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.234, E:I.236, E:D.238, E:D.238

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

NAG.19: 2 residues within 4Å: Chain A: Q.495, N.525 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.525 NAG.23: 1 residues within 4Å: Chain B: N.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.133 NAG.28: 1 residues within 4Å: Chain E: N.525 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.525 NAG.32: 1 residues within 4Å: Chain F: N.133 No protein-ligand interaction detected (PLIP)

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

MN.20: 4 residues within 4Å: Chain B: S.17, D.20, D.21, D.144 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.20, B:D.20, B:D.21, B:D.144, H2O.1 MN.21: 7 residues within 4Å: Chain B: D.13, S.15, A.16, S.17, T.111, E.113 Chain D: D.219 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.219, B:S.15, B:S.17, B:E.113, H2O.1 MN.22: 5 residues within 4Å: Chain B: E.52, N.108, D.110, P.112, E.113 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.52, B:D.110, B:D.110, B:P.112, B:E.113 MN.29: 4 residues within 4Å: Chain F: S.17, D.20, D.21, D.144 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:S.17, F:D.20, F:D.20, F:D.21, F:D.144 MN.30: 6 residues within 4Å: Chain F: D.13, S.15, S.17, T.111, E.113 Chain H: D.219 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.15, F:S.17, F:E.113, H2O.1, H2O.1 MN.31: 5 residues within 4Å: Chain F: E.52, N.108, D.110, P.112, E.113 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.52, F:D.110, F:D.110, F:P.112, F:E.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, X. et al., Force interacts with macromolecular structure in activation of TGF-beta. Nature (2017)

Release Date

2017-01-25

Peptides

Integrin alpha-V: AE
Integrin beta-6: BF
Transforming growth factor beta-1: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

D
D

G
G

H
H

Integrin alpha-V

Integrin beta-6

Transforming growth factor beta-1

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