SMTL ID : 5ffg.1

Crystal structure of integrin alpha V beta 6 head

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, E.52 No protein-ligand interaction detected (PLIP)

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.2: 5 residues within 4Å: Chain A: N.232, D.234, D.257, K.259, N.260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.232, A:D.234 NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: P.452, N.459, T.461, C.473 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.3: 7 residues within 4Å: Chain A: A.213, Q.214, F.217, Y.254, S.263, L.264, N.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Water bridges: A:Y.256

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN.5: 3 residues within 4Å: Chain A: S.523, N.525, R.567 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, H2O.1 CA.7: 6 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357, N.377 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.349, A:D.351, A:D.353, A:F.355, H2O.2 CA.8: 5 residues within 4Å: Chain A: D.414, D.416, N.418, Y.420, D.422 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.414, A:D.416, A:Y.420, A:D.422, H2O.1 CA.9: 6 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238, D.257 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.14: 4 residues within 4Å: Chain B: S.17, D.20, D.21, K.228 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.17, B:D.21, B:K.228, H2O.8, H2O.9 CA.15: 6 residues within 4Å: Chain B: D.13, S.15, S.17, E.113, D.144, A.145 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.13, B:S.15, B:E.113, B:D.144, H2O.8

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

NAG.10: 3 residues within 4Å: Chain A: F.559, P.584, N.586 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.559 Hydrogen bonds: A:N.586 NAG.16: 2 residues within 4Å: Chain B: K.126, N.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.126, B:K.126

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

SO4.11: 2 residues within 4Å: Chain A: R.510, P.520 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.510

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.12: 7 residues within 4Å: Chain A: K.506, G.507, A.508, I.509, F.549, R.550, D.551 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.509, A:R.550, A:D.551

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 4 residues within 4Å: Chain A: Y.516, S.517, H.522, L.539 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.517, A:H.522 PEG.17: 1 residues within 4Å: Chain B: Q.205 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.205 Water bridges: B:L.226

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: A
Integrin beta-6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-V

Integrin beta-6

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