SMTL ID : 4um9.2 (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

4 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: 7 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: P.451, N.458, T.460, C.461, C.472, F.473, N.474 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.474, A:N.474 NAG-NAG.5: 4 residues within 4Å: Chain A: Q.494, S.522, N.524, D.564 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 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: 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(Non-functional Binders)

NAG-NAG-BMA-MAN.2: 5 residues within 4Å: Chain A: N.232, D.257, K.259, N.260, S.262 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.3: 7 residues within 4Å: Chain A: A.213, Q.214, F.217, Y.254, S.263, L.264, N.266 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.213, A:F.217 Water bridges: A:Q.214

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

SO4.7: 2 residues within 4Å: Chain A: P.488, R.489 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.489 Salt bridges: A:R.489 SO4.8: 7 residues within 4Å: Chain A: S.12, G.13, E.15, R.398, V.429, D.430, R.431 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.13, A:D.430 Salt bridges: A:R.398, A:R.431 SO4.9: 4 residues within 4Å: Chain A: 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 SO4.14: 1 residues within 4Å: Chain B: H.277 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.277

6 x CA: CALCIUM ION(Non-covalent)

CA.10: 6 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238, D.257 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.11: 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.12: 5 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.351, A:D.353, A:F.355, A:D.357, H2O.1 CA.13: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:D.421, A:D.421 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 CA.17: 5 residues within 4Å: Chain B: S.127, M.128, 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.131, H2O.5

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 4 residues within 4Å: Chain B: S.125, S.127, E.223 Chain C: D.6 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.6, B:S.125, B:E.223, H2O.4, H2O.4

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

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 NAG.20: 3 residues within 4Å: Chain A: S.305 Chain B: G.368, N.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.305

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
A

B
B

C
E

Integrin alpha-V heavy chain

Integrin beta-6

Latency-associated peptide

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