SMTL ID : 4um8.1 (1 other biounit)

Crystal structure of alpha V beta 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

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.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)

1 x NAG- NAG- BMA- MAN- MAN: 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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain A: N.232, D.257, K.259, N.260, Y.265, S.323, G.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.265, A:Y.265, A:S.323

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: 8 residues within 4Å: Chain A: R.211, A.213, Q.214, F.217, Y.254, S.263, L.264, N.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Hydrophobic interactions: A:A.213

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-functional Binders)

NAG-NAG-BMA.4: 6 residues within 4Å: Chain A: N.458, T.460, C.461, C.472, F.473, N.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.474

1 x NAG- NAG- BMA- MAN- MAN: 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(Non-covalent)

NAG-NAG-BMA-MAN-MAN.5: 2 residues within 4Å: Chain A: N.524, D.564 No protein-ligand interaction detected (PLIP)

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.6: 4 residues within 4Å: Chain A: F.558, E.560, P.583, N.585 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: N.77, S.90 Ligand excluded by PLIP

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

SO4.8: 2 residues within 4Å: Chain A: P.488, R.489 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.489, A:K.490 Salt bridges: A:R.489 SO4.9: 5 residues within 4Å: Chain A: F.337, Y.364, K.369 Chain B: P.288, Q.314 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.369 Hydrogen bonds: B:Q.314 SO4.10: 2 residues within 4Å: Chain A: G.418, G.485 No protein-ligand interaction detected (PLIP)

1 x NI: NICKEL (II) ION(Non-covalent)

NI.11: 1 residues within 4Å: Chain A: H.591 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.591

5 x CA: CALCIUM ION(Non-covalent)

CA.12: 7 residues within 4Å: Chain A: D.230, F.231, 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.2 CA.13: 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.288, A:Y.290, A:D.292, A:D.292, H2O.2 CA.14: 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.15: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.415, A:Y.419, A:D.421, A:D.421 CA.18: 4 residues within 4Å: Chain B: S.144, D.147, D.148, K.355 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.144, B:D.147, B:D.147, B:D.148, B:K.355

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.16: 5 residues within 4Å: Chain B: V.82, P.106, T.120, L.121, Q.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.122

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 5 residues within 4Å: Chain B: D.140, S.142, S.144, E.240, D.271 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.140, B:S.142, B:E.240, B:D.271

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

NAG.19: 1 residues within 4Å: Chain B: N.260 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.260

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: 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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