SMTL ID : 1z7z.3 (3 other biounits)

Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 8.00 Å

Oligo State

hetero-6-6-6-6-6-mer

Ligands

6 x LEU- ILE- GLY- ARG- THR: human coxsackievirus A21(Non-covalent)

LEU-ILE-GLY-ARG-THR.1: 8 residues within 4Å: Chain A: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.84 Hydrogen bonds: A:S.86, A:S.86, A:T.88, A:T.88, A:K.98 LEU-ILE-GLY-ARG-THR.10: 10 residues within 4Å: Chain C: S.233, K.234 Chain F: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.84 Hydrogen bonds: F:S.86, F:S.86, F:T.88, F:T.88, F:K.98 LEU-ILE-GLY-ARG-THR.19: 10 residues within 4Å: Chain K: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 Chain R: S.233, K.234 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:I.84 Hydrogen bonds: K:S.86, K:S.86, K:T.88, K:T.88, K:K.98 LEU-ILE-GLY-ARG-THR.28: 8 residues within 4Å: Chain P: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:I.84 Hydrogen bonds: P:S.86, P:S.86, P:T.88, P:T.88, P:K.98 LEU-ILE-GLY-ARG-THR.37: 8 residues within 4Å: Chain U: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain U Hydrophobic interactions: U:I.84 Hydrogen bonds: U:S.86, U:S.86, U:T.88, U:T.88, U:K.98 LEU-ILE-GLY-ARG-THR.46: 10 residues within 4Å: Chain W: S.233, K.234 Chain Z: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain Z Hydrophobic interactions: Z:I.84 Hydrogen bonds: Z:S.86, Z:S.86, Z:T.88, Z:T.88, Z:K.98

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

NAG.2: 3 residues within 4Å: Chain E: N.103, T.145, L.147 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain E: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain E: G.126, E.127, N.156 Ligand excluded by PLIP NAG.5: 7 residues within 4Å: Chain E: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.6 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain E: Y.83, W.84, T.85 Ligands: NAG.5 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain E: G.239, N.240 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain E: W.97, P.99, N.269 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain E: N.358 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain J: N.103, T.145, L.147 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain J: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain J: G.126, E.127, N.156 Ligand excluded by PLIP NAG.14: 7 residues within 4Å: Chain J: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.15 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain J: Y.83, W.84, T.85 Ligands: NAG.14 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain J: G.239, N.240 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain J: W.97, P.99, N.269 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain J: N.358 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain O: N.103, T.145, L.147 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain O: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain O: G.126, E.127, N.156 Ligand excluded by PLIP NAG.23: 7 residues within 4Å: Chain O: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.24 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain O: Y.83, W.84, T.85 Ligands: NAG.23 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain O: G.239, N.240 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain O: W.97, P.99, N.269 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain O: N.358 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain T: N.103, T.145, L.147 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain T: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain T: G.126, E.127, N.156 Ligand excluded by PLIP NAG.32: 7 residues within 4Å: Chain T: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.33 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain T: Y.83, W.84, T.85 Ligands: NAG.32 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain T: G.239, N.240 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain T: W.97, P.99, N.269 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain T: N.358 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain Y: N.103, T.145, L.147 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain Y: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain Y: G.126, E.127, N.156 Ligand excluded by PLIP NAG.41: 7 residues within 4Å: Chain Y: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain Y: Y.83, W.84, T.85 Ligands: NAG.41 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain Y: G.239, N.240 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain Y: W.97, P.99, N.269 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain Y: N.358 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain 3: N.103, T.145, L.147 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain 3: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain 3: G.126, E.127, N.156 Ligand excluded by PLIP NAG.50: 7 residues within 4Å: Chain 3: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.51 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain 3: Y.83, W.84, T.85 Ligands: NAG.50 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain 3: G.239, N.240 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain 3: W.97, P.99, N.269 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain 3: N.358 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, C. et al., The crystal structure of coxsackievirus a21 and its interaction with icam-1. Structure (2005)

Release Date

2005-08-02

Peptides

human coxsackievirus A21: AFKPUZ
human coxsackievirus A21: BGLQV0
human coxsackievirus A21: CHMRW1
human coxsackievirus A21: DINSX2
Intercellular adhesion molecule-1: EJOTY3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

F
1

K
1

P
1

U
1

Z
1

B
2

G
2

L
2

Q
2

V
2

0
2

C
3

H
3

M
3

R
3

W
3

1
3

D
4

I
4

N
4

S
4

X
4

2
4

E
I

J
I

O
I

T
I

Y
I

3
I

human coxsackievirus A21

human coxsackievirus A21

human coxsackievirus A21

human coxsackievirus A21

Intercellular adhesion molecule-1

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