SMTL ID : 5ner.1

Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O PanAsia - Pose A prime.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 5 residues within 4Å: Chain B: S.70 Chain C: G.59, D.60 Ligands: NAG-MAN.3, MAN.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.70, B:S.70, C:G.59

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 3 residues within 4Å: Chain E: D.257, N.260, S.262 No protein-ligand interaction detected (PLIP)

1 x NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-MAN.3: 7 residues within 4Å: Chain E: A.213, Q.214, F.217 Ligands: MAN-MAN.1, MAN.6, MAN.8, NAG.9 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.214, E:Q.214, E:Q.214 Hydrophobic interactions: E:A.213

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.4: 9 residues within 4Å: Chain E: Y.450, P.451, N.455, N.458, T.460, C.461, C.472, F.473, N.474 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.474, E:N.474

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.5: 6 residues within 4Å: Chain E: F.558, T.582, P.583, A.584, N.585, S.587 No protein-ligand interaction detected (PLIP)

3 x MAN: alpha-D-mannopyranose(Non-functional Binders)(Non-covalent)

MAN.6: 3 residues within 4Å: Ligands: NAG-MAN.3, MAN.7, MAN.8 No protein-ligand interaction detected (PLIP) MAN.7: 2 residues within 4Å: Chain A: S.197 Ligands: MAN.6 No protein-ligand interaction detected (PLIP) MAN.8: 4 residues within 4Å: Ligands: MAN-MAN.1, MAN-MAN.1, NAG-MAN.3, MAN.6 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)

NAG.9: 4 residues within 4Å: Chain E: Y.254, S.263, N.266 Ligands: NAG-MAN.3 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.254, E:S.263, E:S.263 NAG.10: 3 residues within 4Å: Chain E: Q.494, S.522, N.524 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.494, E:S.522, E:S.522, E:S.522, E:N.524 NAG.15: 3 residues within 4Å: Chain F: N.76, S.78, D.79 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.78, F:S.78 NAG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.11: 6 residues within 4Å: Chain E: D.413, D.415, N.417, Y.419, D.421, A.437 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.415, E:D.415, E:Y.419, E:D.421 CA.12: 5 residues within 4Å: Chain E: D.349, D.351, D.353, F.355, D.357 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.349, E:D.351, E:D.353, E:F.355, E:D.357 CA.13: 5 residues within 4Å: Chain E: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.230, E:D.234, E:I.236, E:D.238, E:D.238 CA.14: 5 residues within 4Å: Chain E: D.284, N.286, D.288, Y.290, D.292 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.284, E:D.288, E:Y.290, E:D.292, E:D.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kotecha, A. et al., Rules of engagement between alpha v beta 6 integrin and foot-and-mouth disease virus. Nat Commun (2017)

Release Date

2017-06-21

Peptides

O PanAsia VP1: A
O PanAsia VP2: B
O PanAsia VP3: C
O PanAsia VP4: D
Integrin alpha-V: E
Integrin beta-6: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
A

F
B

O PanAsia VP1

O PanAsia VP2

O PanAsia VP3

O PanAsia VP4

Integrin alpha-V

Integrin beta-6

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