SMTL ID : 9c1g.1

Rhesus rotavirus (consensus structure at 2.36 Angstrom resolution)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-13-2-13-mer

Ligands

13 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 1 residues within 4Å: Chain A: N.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.69 NAG.6: 1 residues within 4Å: Chain B: N.69 No protein-ligand interaction detected (PLIP) NAG.34: 1 residues within 4Å: Chain R: N.69 No protein-ligand interaction detected (PLIP) NAG.39: 1 residues within 4Å: Chain S: N.69 No protein-ligand interaction detected (PLIP) NAG.44: 1 residues within 4Å: Chain T: N.69 No protein-ligand interaction detected (PLIP) NAG.49: 1 residues within 4Å: Chain U: N.69 No protein-ligand interaction detected (PLIP) NAG.54: 1 residues within 4Å: Chain V: N.69 No protein-ligand interaction detected (PLIP) NAG.59: 1 residues within 4Å: Chain W: N.69 No protein-ligand interaction detected (PLIP) NAG.64: 1 residues within 4Å: Chain X: N.69 No protein-ligand interaction detected (PLIP) NAG.69: 1 residues within 4Å: Chain Y: N.69 No protein-ligand interaction detected (PLIP) NAG.74: 1 residues within 4Å: Chain Z: N.69 No protein-ligand interaction detected (PLIP) NAG.79: 1 residues within 4Å: Chain 0: N.69 No protein-ligand interaction detected (PLIP) NAG.84: 1 residues within 4Å: Chain 1: N.69 1 PLIP interactions: 1 interactions with chain 1 Hydrogen bonds: 1:N.69

52 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: L.150, D.151, E.154, E.222, L.224 Chain B: K.290 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.151, A:D.151, A:E.154, A:E.222 CA.3: 6 residues within 4Å: Chain A: Q.177, K.183, D.228, V.229, D.231 Chain B: D.301 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:D.301, A:D.228, A:V.229, A:D.231 CA.4: 5 residues within 4Å: Chain A: G.206, C.207, T.214, E.216 Chain B: D.95 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:G.206, A:T.214, A:E.216, B:D.95 CA.5: 6 residues within 4Å: Chain A: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.270, A:D.270, A:T.272, A:D.274, A:T.277 CA.7: 6 residues within 4Å: Chain 1: K.290 Chain B: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.151, B:E.154, B:E.222, B:L.224 CA.8: 6 residues within 4Å: Chain 1: D.301 Chain B: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain 1 Metal complexes: B:D.228, B:V.229, B:D.231, 1:D.301 CA.9: 5 residues within 4Å: Chain 1: D.95 Chain B: G.206, C.207, T.214, E.216 4 PLIP interactions: 1 interactions with chain 1, 3 interactions with chain B Metal complexes: 1:D.95, B:G.206, B:T.214, B:E.216 CA.10: 6 residues within 4Å: Chain B: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.270, B:D.270, B:T.272, B:D.274, B:T.277 CA.35: 5 residues within 4Å: Chain R: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:D.151, R:E.154, R:E.222, R:L.224 CA.36: 5 residues within 4Å: Chain R: Q.177, K.183, D.228, V.229, D.231 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:D.228, R:V.229, R:D.231 CA.37: 4 residues within 4Å: Chain R: G.206, C.207, T.214, E.216 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:G.206, R:T.214, R:E.216 CA.38: 6 residues within 4Å: Chain R: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:D.270, R:D.270, R:T.272, R:D.274, R:T.277 CA.40: 6 residues within 4Å: Chain S: D.151, E.154, E.222, L.224, V.225 Chain T: K.290 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:D.151, S:E.154, S:E.222, S:L.224 CA.41: 5 residues within 4Å: Chain S: Q.177, D.228, V.229, D.231 Chain T: D.301 4 PLIP interactions: 3 interactions with chain S, 1 interactions with chain T Metal complexes: S:D.228, S:V.229, S:D.231, T:D.301 CA.42: 5 residues within 4Å: Chain S: G.206, C.207, T.214, E.216 Chain T: D.95 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:G.206, S:T.214, S:E.216 CA.43: 6 residues within 4Å: Chain S: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:D.270, S:D.270, S:T.272, S:D.274, S:T.277 CA.45: 6 residues within 4Å: Chain T: D.151, E.154, E.222, L.224, V.225 Chain U: K.290 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.154, T:E.222, T:L.224 CA.46: 6 residues within 4Å: Chain T: Q.177, K.183, D.228, V.229, D.231 Chain U: D.301 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain U Metal complexes: T:D.228, T:V.229, T:D.231, U:D.301 CA.47: 5 residues within 4Å: Chain T: G.206, C.207, T.214, E.216 Chain U: D.95 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain U Metal complexes: T:G.206, T:T.214, T:E.216, U:D.95 CA.48: 6 residues within 4Å: Chain T: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:D.270, T:D.270, T:T.272, T:D.274, T:T.277 CA.50: 6 residues within 4Å: Chain S: K.290 Chain U: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:D.151, U:E.154, U:E.222, U:L.224 CA.51: 6 residues within 4Å: Chain S: D.301 Chain U: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 1 interactions with chain S, 3 interactions with chain U Metal complexes: S:D.301, U:D.228, U:V.229, U:D.231 CA.52: 5 residues within 4Å: Chain S: D.95 Chain U: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain U, 1 interactions with chain S Metal complexes: U:G.206, U:T.214, U:E.216, S:D.95 CA.53: 6 residues within 4Å: Chain U: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:D.270, U:D.270, U:T.272, U:D.274, U:T.277 CA.55: 6 residues within 4Å: Chain V: D.151, E.154, E.222, L.224, V.225 Chain W: K.290 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:D.151, V:E.154, V:E.222, V:L.224 CA.56: 7 residues within 4Å: Chain V: Q.177, N.182, K.183, D.228, V.229, D.231 Chain W: D.301 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain W Metal complexes: V:D.228, V:V.229, V:D.231, W:D.301 CA.57: 5 residues within 4Å: Chain V: G.206, C.207, T.214, E.216 Chain W: D.95 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain W Metal complexes: V:G.206, V:T.214, V:E.216, W:D.95 CA.58: 6 residues within 4Å: Chain V: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:D.270, V:D.270, V:T.272, V:D.274, V:T.277 CA.60: 6 residues within 4Å: Chain W: D.151, E.154, E.222, L.224, V.225 Chain X: K.290 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.154, W:E.222, W:L.224 CA.61: 6 residues within 4Å: Chain W: Q.177, K.183, D.228, V.229, D.231 Chain X: D.301 4 PLIP interactions: 1 interactions with chain X, 3 interactions with chain W Metal complexes: X:D.301, W:D.228, W:V.229, W:D.231 CA.62: 5 residues within 4Å: Chain W: G.206, C.207, T.214, E.216 Chain X: D.95 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:G.206, W:T.214, W:E.216 CA.63: 6 residues within 4Å: Chain W: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:D.270, W:D.270, W:T.272, W:D.274, W:T.277 CA.65: 5 residues within 4Å: Chain X: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:D.151, X:E.154, X:E.222, X:L.224 CA.66: 6 residues within 4Å: Chain V: D.301 Chain X: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain X, 1 interactions with chain V Metal complexes: X:D.228, X:V.229, X:D.231, V:D.301 CA.67: 5 residues within 4Å: Chain V: D.95 Chain X: G.206, C.207, T.214, E.216 4 PLIP interactions: 1 interactions with chain V, 3 interactions with chain X Metal complexes: V:D.95, X:G.206, X:T.214, X:E.216 CA.68: 6 residues within 4Å: Chain X: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:D.270, X:D.270, X:T.272, X:D.274, X:T.277 CA.70: 6 residues within 4Å: Chain Y: D.151, E.154, E.222, L.224, V.225 Chain Z: K.290 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:D.151, Y:E.154, Y:E.222, Y:L.224 CA.71: 6 residues within 4Å: Chain Y: Q.177, K.183, D.228, V.229, D.231 Chain Z: D.301 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain Z Metal complexes: Y:D.228, Y:V.229, Y:D.231, Z:D.301 CA.72: 5 residues within 4Å: Chain Y: G.206, C.207, T.214, E.216 Chain Z: D.95 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain Z Metal complexes: Y:G.206, Y:T.214, Y:E.216, Z:D.95 CA.73: 5 residues within 4Å: Chain Y: D.270, T.272, D.274, P.275, T.277 5 PLIP interactions: 5 interactions with chain Y Metal complexes: Y:D.270, Y:D.270, Y:T.272, Y:D.274, Y:T.277 CA.75: 6 residues within 4Å: Chain 0: K.290 Chain Z: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:D.151, Z:E.154, Z:E.222, Z:L.224 CA.76: 6 residues within 4Å: Chain 0: D.301 Chain Z: Q.177, K.183, D.228, V.229, D.231 4 PLIP interactions: 3 interactions with chain Z, 1 interactions with chain 0 Metal complexes: Z:D.228, Z:V.229, Z:D.231, 0:D.301 CA.77: 5 residues within 4Å: Chain 0: D.95 Chain Z: G.206, C.207, T.214, E.216 4 PLIP interactions: 3 interactions with chain Z, 1 interactions with chain 0 Metal complexes: Z:G.206, Z:T.214, Z:E.216, 0:D.95 CA.78: 5 residues within 4Å: Chain Z: D.270, T.272, D.274, P.275, T.277 5 PLIP interactions: 5 interactions with chain Z Metal complexes: Z:D.270, Z:D.270, Z:T.272, Z:D.274, Z:T.277 CA.80: 5 residues within 4Å: Chain 0: D.151, E.154, E.222, L.224, V.225 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:D.151, 0:E.154, 0:E.222, 0:L.224 CA.81: 7 residues within 4Å: Chain 0: Q.177, N.182, K.183, D.228, V.229, D.231 Chain Y: D.301 4 PLIP interactions: 3 interactions with chain 0, 1 interactions with chain Y Metal complexes: 0:D.228, 0:V.229, 0:D.231, Y:D.301 CA.82: 5 residues within 4Å: Chain 0: G.206, C.207, T.214, E.216 Chain Y: D.95 4 PLIP interactions: 3 interactions with chain 0, 1 interactions with chain Y Metal complexes: 0:G.206, 0:T.214, 0:E.216, Y:D.95 CA.83: 7 residues within 4Å: Chain 0: D.270, T.272, A.273, D.274, P.275, T.277, A.278 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:D.270, 0:T.272, 0:D.274, 0:T.277 CA.85: 6 residues within 4Å: Chain 1: D.151, E.154, E.222, L.224, V.225 Chain A: K.290 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:D.151, 1:E.154, 1:E.222, 1:L.224 CA.86: 5 residues within 4Å: Chain 1: Q.177, D.228, V.229, D.231 Chain A: D.301 4 PLIP interactions: 3 interactions with chain 1, 1 interactions with chain A Metal complexes: 1:D.228, 1:V.229, 1:D.231, A:D.301 CA.87: 5 residues within 4Å: Chain 1: G.206, C.207, T.214, E.216 Chain A: D.95 4 PLIP interactions: 3 interactions with chain 1, 1 interactions with chain A Metal complexes: 1:G.206, 1:T.214, 1:E.216, A:D.95 CA.88: 6 residues within 4Å: Chain 1: D.270, T.272, D.274, P.275, T.277, A.278 5 PLIP interactions: 5 interactions with chain 1 Metal complexes: 1:D.270, 1:D.270, 1:T.272, 1:D.274, 1:T.277

18 x ZN: ZINC ION(Non-covalent)

ZN.11: 7 residues within 4Å: Chain E: H.153, K.154 Chain F: H.153, K.154 Chain G: H.153, K.154 Ligands: CL.14 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain G Metal complexes: F:H.153, E:H.153, G:H.153 ZN.12: 5 residues within 4Å: Chain E: L.166, S.169, H.173, S.240, A.241 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.173 ZN.13: 4 residues within 4Å: Chain F: L.166, H.173, S.240, A.241 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.173 ZN.15: 6 residues within 4Å: Chain G: L.166, S.169, H.173, S.240, A.241, W.247 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.173 ZN.16: 6 residues within 4Å: Chain H: H.153, K.154 Chain I: H.153, K.154 Chain J: H.153 Ligands: CL.17 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J, 1 interactions with chain H Metal complexes: I:H.153, J:H.153, H:H.153 ZN.18: 7 residues within 4Å: Chain H: F.164, L.166, S.169, H.173, S.240, A.241, W.247 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.173 ZN.19: 4 residues within 4Å: Chain I: L.166, H.173, S.240, A.241 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.173 ZN.20: 4 residues within 4Å: Chain J: L.166, H.173, S.240, A.241 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:H.173 ZN.21: 7 residues within 4Å: Chain K: H.153, K.154 Chain L: H.153, K.154 Chain M: H.153, K.154 Ligands: CL.22 3 PLIP interactions: 1 interactions with chain M, 1 interactions with chain K, 1 interactions with chain L Metal complexes: M:H.153, K:H.153, L:H.153 ZN.23: 7 residues within 4Å: Chain K: F.164, L.166, S.169, H.173, S.240, A.241, W.247 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:H.173 ZN.24: 5 residues within 4Å: Chain L: L.166, H.173, S.240, A.241, W.247 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:H.173 ZN.25: 6 residues within 4Å: Chain M: L.166, S.169, H.173, S.240, A.241, W.247 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:H.173 ZN.26: 7 residues within 4Å: Chain N: H.153, K.154 Chain O: H.153, K.154 Chain P: H.153, K.154 Ligands: CL.28 3 PLIP interactions: 1 interactions with chain O, 1 interactions with chain P, 1 interactions with chain N Metal complexes: O:H.153, P:H.153, N:H.153 ZN.27: 5 residues within 4Å: Chain 0: Y.53 Chain N: L.166, H.173, S.240, A.241 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:H.173 ZN.29: 5 residues within 4Å: Chain O: L.166, S.169, H.173, S.240, A.241 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:H.173 ZN.30: 5 residues within 4Å: Chain P: L.166, H.173, S.240, A.241 Chain T: Y.53 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:H.173 ZN.31: 3 residues within 4Å: Chain Q: H.153, K.154 Ligands: CL.32 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:H.153 ZN.33: 5 residues within 4Å: Chain Q: L.166, S.169, H.173, S.240, A.241 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:H.173

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

CL.14: 7 residues within 4Å: Chain E: H.153, K.154 Chain F: H.153, K.154 Chain G: H.153, K.154 Ligands: ZN.11 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain H: H.153, K.154 Chain I: H.153, K.154 Chain J: H.153, K.154 Ligands: ZN.16 Ligand excluded by PLIP CL.22: 7 residues within 4Å: Chain K: H.153, K.154 Chain L: H.153, K.154 Chain M: H.153, K.154 Ligands: ZN.21 Ligand excluded by PLIP CL.28: 7 residues within 4Å: Chain N: H.153, K.154 Chain O: H.153, K.154 Chain P: H.153, K.154 Ligands: ZN.26 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain Q: H.153, K.154 Ligands: ZN.31 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jenni, S. et al., Rotavirus structure. To Be Published

Release Date

2025-04-30

Peptides

Outer capsid glycoprotein VP7: ABRSTUVWXYZ01
Inner capsid protein VP2: CD
Intermediate capsid protein VP6: EFGHIJKLMNOPQ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
1

R
P

S
Q

T
R

U
S

V
T

W
U

X
V

Y
W

Z
X

0
Y

1
Z

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

O
M

P
N

Q
O

Outer capsid glycoprotein VP7

Inner capsid protein VP2

Intermediate capsid protein VP6

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