SMTL ID : 7k6v.1

Crystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus (HOV)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-45-mer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: P.218 Chain C: Q.137 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: R.94, K.225 Chain N: R.94 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain B: P.218 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: D.269, A.468 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain D: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain D: P.218 Chain F: Q.137 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain 6: R.94, K.225 Chain F: R.94, K.225 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain G: P.218 Chain I: Q.137 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain G: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain I: R.94, K.225 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain G: E.316 Chain I: V.416, H.417 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain I: R.223, D.269, A.468 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain J: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain J: Q.137 Chain K: P.218 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain L: R.94 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain H: H.91 Chain J: P.218 Chain L: Q.137 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain M: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain M: R.94, K.225 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain K: H.91 Chain M: P.218 Chain O: Q.137 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain 2: H.91 Chain P: P.218 Chain R: Q.137 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain P: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain S: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain C: R.94, K.225 Chain U: R.94, K.225 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain Q: H.91 Chain S: P.218 Chain U: Q.137 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain V: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain V: P.218 Chain X: Q.137 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain Y: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain W: R.94 Chain Y: R.94, K.225 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain 0: Q.137 Chain Y: P.218 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Chain 1: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain 1: R.94 Chain Z: R.94 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain 1: P.218 Chain 3: Q.137 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain 4: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain 4: R.94, K.225 Chain h: R.94, K.225 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain 4: P.218 Chain 6: Q.137 Chain h: H.91 Ligand excluded by PLIP CL.56: 1 residues within 4Å: Chain 6: A.468 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain 7: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.58: 4 residues within 4Å: Chain 9: R.94, K.225 Chain R: R.94, K.225 Ligand excluded by PLIP CL.59: 2 residues within 4Å: Chain 7: P.218 Chain 9: Q.137 Ligand excluded by PLIP CL.61: 2 residues within 4Å: Chain a: P.218 Chain c: Q.137 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain a: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.63: 2 residues within 4Å: Chain 8: R.94 Chain a: R.94 Ligand excluded by PLIP CL.65: 2 residues within 4Å: Chain c: H.460, Q.463 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain c: R.94, K.225 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain b: H.91 Chain d: P.218 Chain f: Q.137 Ligand excluded by PLIP CL.68: 4 residues within 4Å: Chain d: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.70: 2 residues within 4Å: Chain f: H.505, V.508 Ligand excluded by PLIP CL.72: 4 residues within 4Å: Chain g: T.425, K.490, H.492, Q.523 Ligand excluded by PLIP CL.73: 2 residues within 4Å: Chain g: P.218 Chain i: Q.137 Ligand excluded by PLIP

22 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.5: 2 residues within 4Å: Chain C: H.460 Chain U: H.460 Ligand excluded by PLIP CD.7: 2 residues within 4Å: Chain B: H.460 Chain D: H.460 Ligand excluded by PLIP CD.10: 3 residues within 4Å: Chain 6: H.460 Chain F: H.460, Q.463 Ligand excluded by PLIP CD.12: 2 residues within 4Å: Chain E: H.460 Chain G: H.460 Ligand excluded by PLIP CD.18: 2 residues within 4Å: Chain H: H.460 Chain J: H.460 Ligand excluded by PLIP CD.23: 2 residues within 4Å: Chain K: H.460 Chain M: H.460 Ligand excluded by PLIP CD.27: 2 residues within 4Å: Chain A: H.460 Chain N: H.460 Ligand excluded by PLIP CD.28: 1 residues within 4Å: Chain O: Q.463 Ligand excluded by PLIP CD.29: 2 residues within 4Å: Chain 2: H.460 Chain P: H.460 Ligand excluded by PLIP CD.32: 3 residues within 4Å: Chain 9: H.460, Q.463 Chain R: H.460 Ligand excluded by PLIP CD.33: 2 residues within 4Å: Chain Q: H.460 Chain S: H.460 Ligand excluded by PLIP CD.35: 2 residues within 4Å: Chain T: H.460 Chain V: H.460 Ligand excluded by PLIP CD.39: 1 residues within 4Å: Chain X: H.460 Ligand excluded by PLIP CD.41: 2 residues within 4Å: Chain W: H.460 Chain Y: H.460 Ligand excluded by PLIP CD.46: 2 residues within 4Å: Chain 1: H.460 Chain Z: H.460 Ligand excluded by PLIP CD.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.51: 2 residues within 4Å: Chain 4: H.460 Chain h: H.460 Ligand excluded by PLIP CD.54: 2 residues within 4Å: Chain 5: H.460 Chain 7: H.460 Ligand excluded by PLIP CD.60: 2 residues within 4Å: Chain 8: H.460 Chain a: H.460 Ligand excluded by PLIP CD.64: 2 residues within 4Å: Chain b: H.460 Chain d: H.460 Ligand excluded by PLIP CD.69: 1 residues within 4Å: Chain f: H.460 Ligand excluded by PLIP CD.71: 2 residues within 4Å: Chain e: H.460 Chain g: H.460 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.45: 5 residues within 4Å: Chain 1: D.84, Q.170, S.222, R.223, P.467 2 PLIP interactions: 2 interactions with chain 1 Hydrogen bonds: 1:D.84, 1:S.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, L. et al., Crystal structure of GII.4 Norovirus capsid reveals inherent conformational flexibility of the capsid protein. To Be Published

Release Date

2022-03-02

Peptides

Capsid protein VP1: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghi

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
AB

C
AC

D
BA

E
BB

F
BC

G
CA

H
CB

I
CC

J
DA

K
DB

L
DC

M
EA

N
EB

O
EC

P
FA

Q
FB

R
FC

S
GA

T
GB

U
GC

V
HA

W
HB

X
HC

Y
IA

Z
IB

0
IC

1
JA

2
JB

3
JC

4
KA

5
KB

6
KC

7
LA

8
LB

9
LC

a
MA

b
MB

c
MC

d
NA

e
NB

f
NC

g
OA

h
OB

i
OC

Capsid protein VP1

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