SMTL ID : 4um9.1 (1 other biounit)

Crystal structure of alpha V beta 6 with peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 4 residues within 4Å: Chain A: D.234, D.257, K.259, N.260 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.234 NAG-NAG.4: 4 residues within 4Å: Chain A: F.558, E.560, P.583, N.585 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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN.2: 8 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, N.266 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.213, A:F.217 Hydrogen bonds: A:Q.214, A:Q.214

1 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(Non-covalent)

NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: Y.450, P.451, N.458, T.460, C.461, C.472, N.474 Ligands: MAN.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.474

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

SO4.5: 5 residues within 4Å: Chain A: G.49, N.77, F.88, K.89, S.90 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.77, A:K.89, A:S.90, A:S.90, A:S.90 SO4.6: 3 residues within 4Å: Chain A: S.528, G.531, L.532 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.528, A:L.532

6 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421, A.437 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.415, A:D.415, A:Y.419, A:D.421, H2O.1 CA.8: 5 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.349, A:D.351, A:D.353, A:F.355, A:D.357 CA.9: 5 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.230, A:D.234, A:I.236, A:D.238, H2O.1 CA.10: 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.15: 4 residues within 4Å: Chain B: S.127, D.130, D.131, K.338 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.127, B:D.130, B:D.130, H2O.3 CA.16: 5 residues within 4Å: Chain B: E.162, N.218, D.220, P.222, E.223 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.162, B:D.220, B:D.220, B:P.222, B:E.223

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

NAG.11: 6 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.44, A:E.52, A:E.52 NAG.13: 3 residues within 4Å: Chain A: Q.494, S.522, N.524 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.494, A:N.524 NAG.17: 2 residues within 4Å: Chain B: N.31, Q.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.31, B:Q.54 NAG.18: 3 residues within 4Å: Chain B: N.80, S.82, D.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.80, B:S.82 NAG.19: 1 residues within 4Å: Chain B: N.243 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.243

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.12: 4 residues within 4Å: Chain A: E.448, Y.450, R.476 Ligands: NAG-NAG-BMA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.448, A:R.476

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 5 residues within 4Å: Chain B: D.123, S.125, S.127, E.223 Chain C: D.6 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:S.125, C:D.6, H2O.3, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, X. et al., Structural Determinants of Integrin Beta-Subunit Specificity for Latent Tgf-Beta. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-11-12

Peptides

Integrin alpha-V heavy chain: A
Integrin beta-6: B
Latency-associated peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

Integrin alpha-V heavy chain

Integrin beta-6

Latency-associated peptide

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