SMTL ID : 3jb3.3 (3 other biounits)

Atomic model of cytoplasmic polyhedrosis virus with SAM, GTP and ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

hetero-6-12-12-mer

Ligands

12 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 17 residues within 4Å: Chain A: N.526, S.528, M.532, G.562, A.563, E.564, E.566, G.588, D.589, R.590, V.598, R.599, V.600, D.616, I.617, N.618, E.631 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.526, A:S.528, A:E.564, A:E.564, A:E.564, A:E.566, A:E.566, A:D.589, A:R.590, A:R.599, A:V.600, A:V.600, A:D.616, A:N.618 Salt bridges: A:E.564, A:D.616 SAM.2: 20 residues within 4Å: Chain A: K.838, Y.842, I.861, G.862, R.864, A.867, D.868, I.881, D.882, P.883, A.884, F.904, F.906, I.922, A.923, V.924, N.927, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.923 Hydrogen bonds: A:Y.842, A:G.862, A:R.864, A:R.864, A:F.904, A:F.904, A:I.922 SAM.6: 17 residues within 4Å: Chain F: N.526, S.528, M.532, G.562, A.563, E.564, E.566, G.588, D.589, R.590, V.598, R.599, V.600, D.616, I.617, N.618, E.631 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:N.526, F:S.528, F:E.564, F:E.564, F:E.564, F:E.566, F:E.566, F:D.589, F:R.590, F:R.599, F:V.600, F:V.600, F:D.616, F:N.618 Salt bridges: F:E.564, F:D.616 SAM.7: 20 residues within 4Å: Chain F: K.838, Y.842, I.861, G.862, R.864, A.867, D.868, I.881, D.882, P.883, A.884, F.904, F.906, I.922, A.923, V.924, N.927, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:A.923 Hydrogen bonds: F:Y.842, F:G.862, F:R.864, F:R.864, F:F.904, F:F.904, F:I.922 SAM.11: 17 residues within 4Å: Chain K: N.526, S.528, M.532, G.562, A.563, E.564, E.566, G.588, D.589, R.590, V.598, R.599, V.600, D.616, I.617, N.618, E.631 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:N.526, K:S.528, K:E.564, K:E.564, K:E.564, K:E.566, K:E.566, K:D.589, K:R.590, K:R.599, K:V.600, K:V.600, K:D.616, K:N.618 Salt bridges: K:E.564, K:D.616 SAM.12: 20 residues within 4Å: Chain K: K.838, Y.842, I.861, G.862, R.864, A.867, D.868, I.881, D.882, P.883, A.884, F.904, F.906, I.922, A.923, V.924, N.927, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:A.923 Hydrogen bonds: K:Y.842, K:G.862, K:R.864, K:R.864, K:F.904, K:F.904, K:I.922 SAM.16: 17 residues within 4Å: Chain P: N.526, S.528, M.532, G.562, A.563, E.564, E.566, G.588, D.589, R.590, V.598, R.599, V.600, D.616, I.617, N.618, E.631 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:N.526, P:S.528, P:E.564, P:E.564, P:E.566, P:E.566, P:D.589, P:R.590, P:R.599, P:V.600, P:V.600, P:D.616, P:N.618 Salt bridges: P:E.564, P:D.616 SAM.17: 20 residues within 4Å: Chain P: K.838, Y.842, I.861, G.862, R.864, A.867, D.868, I.881, D.882, P.883, A.884, F.904, F.906, I.922, A.923, V.924, N.927, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain P Hydrophobic interactions: P:A.923 Hydrogen bonds: P:Y.842, P:G.862, P:R.864, P:R.864, P:F.904, P:F.904, P:I.922 SAM.21: 17 residues within 4Å: Chain U: N.526, S.528, M.532, G.562, A.563, E.564, E.566, G.588, D.589, R.590, V.598, R.599, V.600, D.616, I.617, N.618, E.631 16 PLIP interactions: 16 interactions with chain U Hydrogen bonds: U:N.526, U:S.528, U:E.564, U:E.564, U:E.564, U:E.566, U:E.566, U:D.589, U:R.590, U:R.599, U:V.600, U:V.600, U:D.616, U:N.618 Salt bridges: U:E.564, U:D.616 SAM.22: 20 residues within 4Å: Chain U: K.838, Y.842, I.861, G.862, R.864, A.867, D.868, I.881, D.882, P.883, A.884, F.904, F.906, I.922, A.923, V.924, N.927, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain U Hydrophobic interactions: U:A.923 Hydrogen bonds: U:Y.842, U:G.862, U:R.864, U:R.864, U:F.904, U:F.904, U:I.922 SAM.26: 17 residues within 4Å: Chain Z: N.526, S.528, M.532, G.562, A.563, E.564, E.566, G.588, D.589, R.590, V.598, R.599, V.600, D.616, I.617, N.618, E.631 17 PLIP interactions: 17 interactions with chain Z Hydrogen bonds: Z:N.526, Z:S.528, Z:E.564, Z:E.564, Z:E.564, Z:E.566, Z:E.566, Z:D.589, Z:R.590, Z:R.599, Z:V.600, Z:V.600, Z:D.616, Z:N.618, Z:E.631 Salt bridges: Z:E.564, Z:D.616 SAM.27: 20 residues within 4Å: Chain Z: K.838, Y.842, I.861, G.862, R.864, A.867, D.868, I.881, D.882, P.883, A.884, F.904, F.906, I.922, A.923, V.924, N.927, E.928, P.929, Y.992 8 PLIP interactions: 8 interactions with chain Z Hydrophobic interactions: Z:A.923 Hydrogen bonds: Z:Y.842, Z:G.862, Z:R.864, Z:R.864, Z:F.904, Z:F.904, Z:I.922

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 7 residues within 4Å: Chain A: Y.268, R.271, S.301, D.302, Y.305, Y.316, Y.320 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.268, A:R.271, A:D.302, A:D.302, A:D.302, A:Y.305, A:Y.316, A:Y.320 Salt bridges: A:R.271, A:R.271 pi-Stacking: A:Y.305, A:Y.305 pi-Cation interactions: A:R.271, A:R.271 ATP.8: 7 residues within 4Å: Chain F: Y.268, R.271, S.301, D.302, Y.305, Y.316, Y.320 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Y.268, F:R.271, F:D.302, F:D.302, F:D.302, F:Y.305, F:Y.316, F:Y.320 Salt bridges: F:R.271, F:R.271 pi-Stacking: F:Y.305, F:Y.305 pi-Cation interactions: F:R.271, F:R.271 ATP.13: 7 residues within 4Å: Chain K: Y.268, R.271, S.301, D.302, Y.305, Y.316, Y.320 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:Y.268, K:R.271, K:D.302, K:D.302, K:D.302, K:D.302, K:Y.305 Salt bridges: K:R.271, K:R.271 pi-Stacking: K:Y.305, K:Y.305 pi-Cation interactions: K:R.271, K:R.271 ATP.18: 7 residues within 4Å: Chain P: Y.268, R.271, S.301, D.302, Y.305, Y.316, Y.320 11 PLIP interactions: 11 interactions with chain P Hydrogen bonds: P:Y.268, P:R.271, P:D.302, P:D.302, P:D.302 Salt bridges: P:R.271, P:R.271 pi-Stacking: P:Y.305, P:Y.305 pi-Cation interactions: P:R.271, P:R.271 ATP.23: 7 residues within 4Å: Chain U: Y.268, R.271, S.301, D.302, Y.305, Y.316, Y.320 13 PLIP interactions: 13 interactions with chain U Hydrogen bonds: U:Y.268, U:R.271, U:D.302, U:D.302, U:D.302, U:D.302, U:Y.305 Salt bridges: U:R.271, U:R.271 pi-Stacking: U:Y.305, U:Y.305 pi-Cation interactions: U:R.271, U:R.271 ATP.28: 7 residues within 4Å: Chain Z: Y.268, R.271, S.301, D.302, Y.305, Y.316, Y.320 15 PLIP interactions: 15 interactions with chain Z Hydrogen bonds: Z:Y.268, Z:Y.268, Z:R.271, Z:D.302, Z:D.302, Z:D.302, Z:D.302, Z:Y.305, Z:Y.316 Salt bridges: Z:R.271, Z:R.271 pi-Stacking: Z:Y.305, Z:Y.305 pi-Cation interactions: Z:R.271, Z:R.271

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.4: 17 residues within 4Å: Chain A: R.12, Y.59, N.61, W.115, M.116, P.165, I.166, T.167, Y.179, H.208, H.212, W.213, H.217, F.219, K.234, R.255 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.12, A:Y.59, A:N.61, A:N.61, A:N.61, A:Y.179 Salt bridges: A:H.208, A:H.212, A:H.217, A:K.234, A:K.234, A:R.255, A:R.255 pi-Stacking: A:Y.59 GTP.9: 17 residues within 4Å: Chain F: R.12, Y.59, N.61, W.115, M.116, P.165, I.166, T.167, Y.179, H.208, H.212, W.213, H.217, F.219, K.234, R.255 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:R.12, F:Y.59, F:N.61, F:N.61, F:N.61, F:Y.179 Salt bridges: F:H.208, F:H.212, F:H.217, F:K.234, F:K.234, F:R.255, F:R.255 pi-Stacking: F:Y.59 GTP.14: 17 residues within 4Å: Chain K: R.12, Y.59, N.61, W.115, M.116, P.165, I.166, T.167, Y.179, H.208, H.212, W.213, H.217, F.219, K.234, R.255 Ligands: MG.15 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:R.12, K:Y.59, K:N.61, K:N.61, K:N.61 Salt bridges: K:H.208, K:H.212, K:H.217, K:K.234, K:K.234, K:R.255, K:R.255 pi-Stacking: K:Y.59 GTP.19: 17 residues within 4Å: Chain P: R.12, Y.59, N.61, W.115, M.116, P.165, I.166, T.167, Y.179, H.208, H.212, W.213, H.217, F.219, K.234, R.255 Ligands: MG.20 13 PLIP interactions: 13 interactions with chain P Hydrogen bonds: P:R.12, P:N.61, P:N.61, P:N.61, P:Y.179 Salt bridges: P:H.208, P:H.212, P:H.217, P:K.234, P:K.234, P:R.255, P:R.255 pi-Stacking: P:Y.59 GTP.24: 17 residues within 4Å: Chain U: R.12, Y.59, N.61, W.115, M.116, P.165, I.166, T.167, Y.179, H.208, H.212, W.213, H.217, F.219, K.234, R.255 Ligands: MG.25 13 PLIP interactions: 13 interactions with chain U Hydrogen bonds: U:R.12, U:Y.59, U:N.61, U:N.61, U:N.61 Salt bridges: U:H.208, U:H.212, U:H.217, U:K.234, U:K.234, U:R.255, U:R.255 pi-Stacking: U:Y.59 GTP.29: 17 residues within 4Å: Chain Z: R.12, Y.59, N.61, W.115, M.116, P.165, I.166, T.167, Y.179, H.208, H.212, W.213, H.217, F.219, K.234, R.255 Ligands: MG.30 13 PLIP interactions: 13 interactions with chain Z Hydrogen bonds: Z:R.12, Z:Y.59, Z:N.61, Z:N.61, Z:N.61 Salt bridges: Z:H.208, Z:H.212, Z:H.217, Z:K.234, Z:K.234, Z:R.255, Z:R.255 pi-Stacking: Z:Y.59

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: D.254 Ligands: GTP.4 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain F: D.254 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain K: D.254 Ligands: GTP.14 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain P: D.254 Ligands: GTP.19 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain U: D.254 Ligands: GTP.24 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain Z: D.254 Ligands: GTP.29 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., A putative ATPase mediates RNA transcription and capping in a dsRNA virus. Elife (2015)

Release Date

2015-08-12

Peptides

Structural protein VP3: AFKPUZ
Capsid protein VP1: BCGHLMQRVW01
Viral structural protein 5: DEIJNOSTXY23

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

K
A

P
A

U
A

Z
A

B
B

C
C

G
B

H
C

L
B

M
C

Q
B

R
C

V
B

W
C

0
B

1
C

D
D

E
E

I
D

J
E

N
D

O
E

S
D

T
E

X
D

Y
E

2
D

3
E

Structural protein VP3

Capsid protein VP1

Viral structural protein 5

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