SMTL ID : 6om2.1

Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

hetero-2-2-2-mer

Ligands

3 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: 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-BMA.5: 3 residues within 4Å: Chain B: N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain D: N.191, T.193, E.194 No protein-ligand interaction detected (PLIP)

3 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.2: 15 residues within 4Å: Chain A: N.232, G.233, D.234, D.257, K.259, N.260, S.262, S.323, G.324 Chain C: G.287, D.288, D.289, Y.290, N.356 Ligands: PEG.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.289, C:D.289, C:N.356 Water bridges: C:D.284 NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 9 residues within 4Å: Chain C: E.15, G.16, S.17, K.42, A.43, N.44, V.51, E.52, H.91 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.9: 11 residues within 4Å: Chain C: E.449, Y.451, P.452, N.459, T.461, C.473, F.474, N.475, E.538, L.539, I.540 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.451, C:Y.451, C:Y.451 Hydrophobic interactions: C:T.461

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

NAG-NAG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain A: T.212, A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, Y.265, N.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214, A:T.212 Water bridges: A:R.211, A:R.211, A:T.212 Hydrophobic interactions: A:F.217

1 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.4: 9 residues within 4Å: Chain A: E.449, Y.451, P.452, N.456, N.459, T.461, C.473, F.474, R.477 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.477

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.7: 10 residues within 4Å: Chain A: E.190, K.194, N.205, N.206 Chain C: N.232, D.257, N.260, S.262, S.263, L.264 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.205, A:N.206, C:N.232 NAG-NAG.10: 6 residues within 4Å: Chain C: K.491, N.493, N.525, T.527, D.565, T.568 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.493 NAG-NAG.11: 3 residues within 4Å: Chain C: F.559, A.585, N.586 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain D: Q.75, L.100, Y.103, K.232, E.233, N.414, E.415 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.100 Hydrogen bonds: D:E.233

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.8: 9 residues within 4Å: Chain C: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, Y.265, N.266 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.214, C:Q.214 Hydrophobic interactions: C:F.217

10 x CA: CALCIUM ION(Non-covalent)

CA.14: 7 residues within 4Å: Chain A: D.230, F.231, 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:D.234, A:I.236, A:D.238 CA.15: 6 residues within 4Å: Chain A: D.284, I.285, 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.16: 7 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357, N.377, G.378 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.17: 7 residues within 4Å: Chain A: D.414, I.415, D.416, N.418, Y.420, D.422, A.438 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.22: 6 residues within 4Å: Chain B: D.151, N.207, D.209, T.210, P.211, E.212 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.151, B:D.209, B:D.209, B:P.211, B:E.212 CA.24: 7 residues within 4Å: Chain C: D.230, F.231, N.232, D.234, I.236, D.238, D.257 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.230, C:D.234, C:D.234, C:I.236, C:D.238 CA.25: 6 residues within 4Å: Chain C: D.284, I.285, N.286, D.288, Y.290, D.292 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.284, C:D.288, C:Y.290, C:D.292, H2O.4 CA.26: 7 residues within 4Å: Chain C: D.349, L.350, D.351, D.353, F.355, D.357, N.377 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.351, C:D.353, C:F.355, C:D.357, H2O.4 CA.27: 7 residues within 4Å: Chain C: D.414, I.415, D.416, N.418, Y.420, D.422, A.438 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.414, C:D.416, C:Y.420, C:D.422, C:D.422 CA.30: 6 residues within 4Å: Chain D: D.151, N.207, D.209, T.210, P.211, E.212 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.151, D:D.209, D:D.209, D:P.211, D:E.212

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

NAG.18: 2 residues within 4Å: Chain A: Q.495, N.525 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.495, A:N.525 NAG.19: 4 residues within 4Å: Chain A: K.502, 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.29: 3 residues within 4Å: Chain D: N.92, M.94, N.389 No protein-ligand interaction detected (PLIP)

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

PEG.20: 2 residues within 4Å: Chain A: Y.516, H.522 No protein-ligand interaction detected (PLIP) PEG.28: 10 residues within 4Å: Chain A: D.234 Chain C: N.286, D.288, Y.290, L.319, Q.320, R.321, A.322, Q.327 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.2 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.286, C:A.322, C:Q.327 Water bridges: C:Q.320

2 x MG: MAGNESIUM ION(Non-covalent)

MG.21: 5 residues within 4Å: Chain B: D.112, S.114, S.116, E.212 Chain E: D.5 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: B:S.114, B:S.116, B:E.212, E:D.5, H2O.3, H2O.4 MG.31: 5 residues within 4Å: Chain D: D.112, S.114, S.116, E.212 Chain F: D.5 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: D:S.114, D:S.116, D:E.212, F:D.5, H2O.8, H2O.8

1 x GLY: GLYCINE(Non-covalent)

GLY.23: 2 residues within 4Å: Chain C: L.595, T.596 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.595

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., General structural features that regulate integrin affinity revealed by atypical alpha V beta 8. Nat Commun (2019)

Release Date

2019-12-11

Peptides

Integrin alpha-V: AC
Integrin beta-8: BD
proTGF-beta1 RGD peptide: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Integrin alpha-V

Integrin beta-8

proTGF-beta1 RGD peptide