SMTL ID : 8olc.1

SA11 Rotavirus Trypsinized Triple Layered Particle

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-13-13-2-mer

Ligands

26 x CA: CALCIUM ION

CA.1: 5 residues within 4Å: Chain A: Q.177, D.179, D.228, V.229 Chain B: D.301 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.301, A:D.228, A:V.229 CA.3: 3 residues within 4Å: Chain A: G.206, T.214 Chain B: D.95 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.95, A:G.206, A:T.214 CA.4: 3 residues within 4Å: Chain B: G.206, T.214, E.216 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.206, B:T.214, B:E.216 CA.5: 6 residues within 4Å: Chain B: Q.177, D.179, D.228, V.229, D.231 Chain C: D.301 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.228, B:V.229, B:D.231, B:D.231 CA.7: 6 residues within 4Å: Chain A: D.301 Chain C: Q.177, D.179, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.228, C:V.229, C:D.231, C:D.231, A:D.301 CA.8: 4 residues within 4Å: Chain A: D.95 Chain C: G.206, T.214, E.216 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.214 CA.10: 3 residues within 4Å: Chain D: G.206, T.214, E.216 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.214, D:E.216 CA.11: 6 residues within 4Å: Chain D: Q.177, D.179, D.228, V.229, D.231 Chain E: D.301 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Metal complexes: E:D.301, D:D.228, D:D.231, D:D.231 CA.12: 3 residues within 4Å: Chain E: G.206, T.214, E.216 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:G.206, E:T.214, E:E.216 CA.13: 7 residues within 4Å: Chain E: Q.177, D.179, N.182, D.228, V.229, D.231 Chain F: D.301 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.228, E:D.231 CA.15: 6 residues within 4Å: Chain D: D.301 Chain F: Q.177, D.179, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Metal complexes: F:D.228, F:V.229, F:D.231, D:D.301 CA.16: 4 residues within 4Å: Chain D: D.95 Chain F: G.206, T.214, E.216 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:G.206, F:E.216 CA.17: 3 residues within 4Å: Chain G: T.214, E.216 Chain H: D.95 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Metal complexes: G:T.214, G:E.216, H:D.95 CA.18: 5 residues within 4Å: Chain G: Q.177, D.228, V.229, D.231 Chain H: D.301 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G Metal complexes: H:D.301, G:D.228, G:V.229, G:D.231 CA.20: 3 residues within 4Å: Chain H: G.206, T.214, E.216 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:G.206, H:T.214 CA.21: 5 residues within 4Å: Chain H: Q.177, D.179, D.228, V.229 Chain I: D.301 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.228, H:V.229 CA.23: 5 residues within 4Å: Chain G: D.301 Chain I: Q.177, D.228, V.229, D.231 5 PLIP interactions: 1 interactions with chain G, 4 interactions with chain I Metal complexes: G:D.301, I:D.228, I:V.229, I:D.231, I:D.231 CA.24: 3 residues within 4Å: Chain G: D.95 Chain I: G.206, T.214 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:G.206, I:T.214 CA.26: 4 residues within 4Å: Chain J: G.206, T.214, E.216 Chain K: D.95 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:G.206, J:T.214, J:E.216 CA.27: 5 residues within 4Å: Chain J: Q.177, D.228, V.229, D.231 Chain K: D.301 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain K Metal complexes: J:D.228, J:V.229, J:D.231, J:D.231, K:D.301 CA.29: 5 residues within 4Å: Chain K: Q.177, D.228, V.229, D.231 Chain L: D.301 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain K Metal complexes: L:D.301, K:D.228, K:V.229, K:D.231 CA.30: 3 residues within 4Å: Chain K: G.206, T.214, E.216 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:G.206, K:T.214, K:E.216 CA.32: 3 residues within 4Å: Chain J: D.95 Chain L: G.206, T.214 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:G.206, L:T.214 CA.33: 5 residues within 4Å: Chain J: D.301 Chain L: Q.177, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain J Metal complexes: L:D.228, L:V.229, L:D.231, L:D.231, J:D.301 CA.35: 3 residues within 4Å: Chain M: G.206, T.214, E.216 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.214 CA.36: 1 residues within 4Å: Chain M: D.301 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.301

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.2: 1 residues within 4Å: Chain B: N.69 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain C: N.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.69 NAG.9: 1 residues within 4Å: Chain D: N.69 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.69 NAG.14: 4 residues within 4Å: Chain F: N.69, S.70, T.71, E.74 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:N.69 Hydrogen bonds: F:N.69, F:E.74 NAG.19: 1 residues within 4Å: Chain H: N.69 No protein-ligand interaction detected (PLIP) NAG.22: 1 residues within 4Å: Chain I: N.69 No protein-ligand interaction detected (PLIP) NAG.25: 1 residues within 4Å: Chain J: N.69 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.69 NAG.28: 1 residues within 4Å: Chain K: N.69 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.69 NAG.31: 1 residues within 4Å: Chain L: N.69 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.69 NAG.34: 1 residues within 4Å: Chain M: N.69 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:N.69

5 x ZN: ZINC ION

ZN.37: 3 residues within 4Å: Chain N: H.153 Chain O: H.153 Chain P: H.153 3 PLIP interactions: 1 interactions with chain O, 1 interactions with chain N, 1 interactions with chain P Metal complexes: O:H.153, N:H.153, P:H.153 ZN.38: 3 residues within 4Å: Chain Q: H.153 Chain R: H.153 Chain S: H.153 3 PLIP interactions: 1 interactions with chain R, 1 interactions with chain Q, 1 interactions with chain S Metal complexes: R:H.153, Q:H.153, S:H.153 ZN.39: 3 residues within 4Å: Chain T: H.153 Chain U: H.153 Chain V: H.153 3 PLIP interactions: 1 interactions with chain V, 1 interactions with chain T, 1 interactions with chain U Metal complexes: V:H.153, T:H.153, U:H.153 ZN.40: 3 residues within 4Å: Chain W: H.153 Chain X: H.153 Chain Y: H.153 3 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain X, 1 interactions with chain W Metal complexes: Y:H.153, X:H.153, W:H.153 ZN.41: 1 residues within 4Å: Chain Z: H.153 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:H.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Asensio-Cob, D. et al., Structural basis of rotavirus spike proteolytic activation. To Be Published

Release Date

2024-09-25

Peptides

Outer capsid glycoprotein VP7: ABCDEFGHIJKLM
Intermediate capsid protein VP6: NOPQRSTUVWXYZ
Inner capsid protein VP2: 01

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
c

B
d

C
e

D
f

E
g

F
h

G
i

H
j

I
k

J
l

K
m

L
n

M
o

N
C

O
D

P
E

Q
F

R
G

S
H

T
I

U
J

V
K

W
L

X
M

Y
N

Z
O

0
A

1
B

Outer capsid glycoprotein VP7

Intermediate capsid protein VP6

Inner capsid protein VP2

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