SMTL ID : 8olb.1

SA11 Rotavirus Non-tripsinized Triple Layered Particle

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-13-13-mer

Ligands

26 x CA: CALCIUM ION

CA.1: 4 residues within 4Å: Chain C: G.206, T.214, E.216 Chain D: D.95 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.214, C:E.216 CA.2: 5 residues within 4Å: Chain C: Q.177, D.228, V.229, D.231 Chain D: D.301 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:D.228, C:V.229, C:D.231, D:D.301 CA.4: 4 residues within 4Å: Chain D: G.206, T.214, E.216 Chain E: D.95 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.206, D:T.214, D:E.216 CA.5: 5 residues within 4Å: Chain D: Q.177, D.228, V.229, D.231 Chain E: D.301 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Metal complexes: D:D.228, D:V.229, E:D.301 CA.7: 5 residues within 4Å: Chain C: D.301 Chain E: Q.177, D.228, V.229, D.231 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Metal complexes: E:D.228, E:V.229, C:D.301 CA.8: 5 residues within 4Å: Chain C: D.95 Chain E: G.206, T.214, F.215, E.216 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:G.206, E:T.214, E:E.216 CA.10: 4 residues within 4Å: Chain F: G.206, T.214, F.215, E.216 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.214, F:E.216 CA.11: 5 residues within 4Å: Chain F: Q.177, D.228, V.229, D.231 Chain G: D.301 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Metal complexes: F:D.228, F:V.229, F:D.231, G:D.301 CA.12: 3 residues within 4Å: Chain G: G.206, T.214 Chain H: D.95 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:G.206, G:T.214 CA.13: 6 residues within 4Å: Chain G: Q.177, D.179, D.228, V.229, D.231 Chain H: D.301 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Metal complexes: G:D.228, G:V.229, G:D.231, H:D.301 CA.15: 5 residues within 4Å: Chain F: D.301 Chain H: Q.177, D.228, V.229, D.231 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain H Metal complexes: F:D.301, H:D.228, H:V.229, H:D.231 CA.16: 4 residues within 4Å: Chain F: D.95 Chain H: G.206, T.214, E.216 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:G.206, H:T.214, H:E.216 CA.17: 4 residues within 4Å: Chain I: G.206, T.214, E.216 Chain J: D.95 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain I Metal complexes: J:D.95, J:D.95, I:G.206, I:E.216 CA.18: 6 residues within 4Å: Chain I: Q.177, D.179, D.228, V.229, D.231 Chain J: D.301 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J Metal complexes: I:D.228, I:V.229, I:D.231, J:D.301 CA.20: 4 residues within 4Å: Chain J: G.206, T.214, E.216 Chain K: D.95 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:G.206, J:E.216 CA.21: 5 residues within 4Å: Chain J: Q.177, D.179, D.228, V.229 Chain K: D.301 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J Metal complexes: K:D.301, J:D.228, J:V.229 CA.23: 6 residues within 4Å: Chain I: D.301 Chain K: Q.177, D.179, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain I Metal complexes: K:D.228, K:V.229, K:D.231, I:D.301 CA.24: 5 residues within 4Å: Chain I: D.95 Chain K: G.206, C.207, T.214, E.216 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:G.206, K:T.214, K:E.216 CA.26: 5 residues within 4Å: Chain L: Q.177, D.228, V.229, D.231 Chain M: D.301 5 PLIP interactions: 1 interactions with chain M, 4 interactions with chain L Metal complexes: M:D.301, L:D.228, L:V.229, L:D.231, L:D.231 CA.27: 4 residues within 4Å: Chain L: G.206, T.214, E.216 Chain M: D.95 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:G.206 CA.29: 3 residues within 4Å: Chain M: G.206, T.214, E.216 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:G.206, M:T.214, M:E.216 CA.30: 6 residues within 4Å: Chain M: Q.177, D.179, D.228, V.229, D.231 Chain N: D.301 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N Metal complexes: M:D.228, M:V.229, M:D.231, N:D.301 CA.32: 6 residues within 4Å: Chain L: D.301 Chain N: Q.177, D.179, D.228, V.229, D.231 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain L Metal complexes: N:D.228, N:V.229, N:D.231, N:D.231, L:D.301 CA.33: 4 residues within 4Å: Chain L: D.95 Chain N: G.206, T.214, E.216 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:G.206, N:T.214 CA.35: 3 residues within 4Å: Chain O: G.206, T.214, E.216 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:G.206, O:T.214, O:E.216 CA.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

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

5 x ZN: ZINC ION

ZN.37: 3 residues within 4Å: Chain P: H.153 Chain Q: H.153 Chain R: H.153 3 PLIP interactions: 1 interactions with chain R, 1 interactions with chain P, 1 interactions with chain Q Metal complexes: R:H.153, P:H.153, Q:H.153 ZN.38: 3 residues within 4Å: Chain S: H.153 Chain T: H.153 Chain U: H.153 3 PLIP interactions: 1 interactions with chain U, 1 interactions with chain T, 1 interactions with chain S Metal complexes: U:H.153, T:H.153, S:H.153 ZN.39: 3 residues within 4Å: Chain V: H.153 Chain W: H.153 Chain X: H.153 3 PLIP interactions: 1 interactions with chain X, 1 interactions with chain V, 1 interactions with chain W Metal complexes: X:H.153, V:H.153, W:H.153 ZN.40: 3 residues within 4Å: Chain 0: H.153 Chain Y: H.153 Chain Z: H.153 3 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain Z, 1 interactions with chain 0 Metal complexes: Y:H.153, Z:H.153, 0:H.153 ZN.41: 1 residues within 4Å: Chain 1: H.153 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1: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

Inner capsid protein VP2: AB
Outer capsid glycoprotein VP7: CDEFGHIJKLMNO
Intermediate capsid protein VP6: PQRSTUVWXYZ01

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
c

D
d

E
e

F
f

G
g

H
h

I
i

J
j

K
k

L
l

M
m

N
n

O
o

P
C

Q
D

R
E

S
F

T
G

U
H

V
I

W
J

X
K

Y
L

Z
M

0
N

1
O

Inner capsid protein VP2

Outer capsid glycoprotein VP7

Intermediate capsid protein VP6

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