SMTL ID : 5nem.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

2 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.1: 4 residues within 4Å: Chain E: N.230, D.255, N.258, S.260 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.2: 8 residues within 4Å: Chain E: A.211, Q.212, F.215, Y.252, S.261, N.264 Ligands: MAN.6, MAN.7 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.211 Hydrogen bonds: E:Q.212

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Post Translational Modification)

MAN-MAN.3: 6 residues within 4Å: Chain B: S.68, D.69, S.70 Chain E: R.209, T.210 Ligands: MAN.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:S.70, B:S.70, E:R.209

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.448, P.449, N.453, N.456, T.458, C.459, C.470, F.471, N.472 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.472, E:N.472

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.554, T.578, P.579, A.580, N.581, S.583 No protein-ligand interaction detected (PLIP)

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

MAN.6: 4 residues within 4Å: Chain C: G.59 Ligands: NAG-NAG-MAN.2, MAN-MAN.3, MAN.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.59 MAN.7: 5 residues within 4Å: Chain C: G.59, D.60 Ligands: NAG-NAG-MAN.2, MAN.6, MAN.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.59 MAN.8: 5 residues within 4Å: Chain A: H.195 Chain C: R.56, D.60, K.84 Ligands: MAN.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.56, C:R.56, C:K.84

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

NAG.9: 3 residues within 4Å: Chain E: Q.492, S.518, N.520 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.492, E:S.518, E:S.518, E:S.518, E:N.520 NAG.14: 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.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.10: 6 residues within 4Å: Chain E: D.411, D.413, N.415, Y.417, D.419, A.435 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.413, E:D.413, E:Y.417, E:D.419 CA.11: 5 residues within 4Å: Chain E: D.347, D.349, D.351, F.353, D.355 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.347, E:D.349, E:D.351, E:F.353, E:D.355 CA.12: 5 residues within 4Å: Chain E: D.228, N.230, D.232, I.234, D.236 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.228, E:D.232, E:I.234, E:D.236, E:D.236 CA.13: 5 residues within 4Å: Chain E: D.282, N.284, D.286, Y.288, D.290 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.282, E:D.286, E:Y.288, E:D.290, E:D.290

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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