SMTL ID : 7z51.3 (2 other biounits)

Tick-borne encephalitis virus Kuutsalo-14

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-18-18-mer

Ligands

18 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 2 residues within 4Å: Chain A: N.154 Chain B: H.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 2 residues within 4Å: Chain A: H.104 Chain B: N.154 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.104 NAG-NAG-FUC.3: 2 residues within 4Å: Chain C: N.154, E.155 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.10: 2 residues within 4Å: Chain G: N.154 Chain H: H.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.11: 2 residues within 4Å: Chain G: H.104 Chain H: N.154 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:H.104 NAG-NAG-FUC.12: 2 residues within 4Å: Chain I: N.154, E.155 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.19: 2 residues within 4Å: Chain M: N.154 Chain N: H.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.20: 2 residues within 4Å: Chain M: H.104 Chain N: N.154 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:H.104 NAG-NAG-FUC.21: 2 residues within 4Å: Chain O: N.154, E.155 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.28: 2 residues within 4Å: Chain S: N.154 Chain T: H.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.29: 2 residues within 4Å: Chain S: H.104 Chain T: N.154 1 PLIP interactions: 1 interactions with chain S Hydrophobic interactions: S:H.104 NAG-NAG-FUC.30: 2 residues within 4Å: Chain U: N.154, E.155 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.37: 2 residues within 4Å: Chain Y: N.154 Chain Z: H.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.38: 2 residues within 4Å: Chain Y: H.104 Chain Z: N.154 1 PLIP interactions: 1 interactions with chain Y Hydrophobic interactions: Y:H.104 NAG-NAG-FUC.39: 2 residues within 4Å: Chain 0: N.154, E.155 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.46: 2 residues within 4Å: Chain 4: N.154 Chain 5: H.104 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.47: 2 residues within 4Å: Chain 4: H.104 Chain 5: N.154 1 PLIP interactions: 1 interactions with chain 4 Hydrophobic interactions: 4:H.104 NAG-NAG-FUC.48: 2 residues within 4Å: Chain 6: N.154, E.155 No protein-ligand interaction detected (PLIP)

36 x CPL: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

CPL.4: 9 residues within 4Å: Chain A: I.410, L.413, T.414, V.415, G.417, H.438, G.442 Chain E: G.10, T.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.410, A:L.413 Salt bridges: A:H.438, A:H.438 CPL.5: 7 residues within 4Å: Chain A: K.405, T.406, G.409, I.410, R.412, A.420, W.421 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.406 Salt bridges: A:R.412 CPL.6: 7 residues within 4Å: Chain B: T.414, V.415, G.417, H.438, M.490 Chain F: G.10, T.13 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.438, B:H.438 CPL.7: 7 residues within 4Å: Chain B: K.405, T.406, G.409, I.410, R.412, W.421, F.423 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.410 Salt bridges: B:K.405, B:R.412 CPL.8: 4 residues within 4Å: Chain C: L.413, T.414, H.438, M.490 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.413 Salt bridges: C:H.438, C:H.438 CPL.9: 7 residues within 4Å: Chain C: K.405, T.406, G.409, I.410, R.412, A.420, F.423 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.410 Salt bridges: C:R.412 CPL.13: 9 residues within 4Å: Chain G: I.410, L.413, T.414, V.415, G.417, H.438, G.442 Chain K: G.10, T.13 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:I.410, G:L.413 Salt bridges: G:H.438, G:H.438 CPL.14: 7 residues within 4Å: Chain G: K.405, T.406, G.409, I.410, R.412, A.420, W.421 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:T.406 Salt bridges: G:R.412 CPL.15: 7 residues within 4Å: Chain H: T.414, V.415, G.417, H.438, M.490 Chain L: G.10, T.13 2 PLIP interactions: 2 interactions with chain H Salt bridges: H:H.438, H:H.438 CPL.16: 7 residues within 4Å: Chain H: K.405, T.406, G.409, I.410, R.412, W.421, F.423 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:I.410 Salt bridges: H:K.405, H:R.412 CPL.17: 4 residues within 4Å: Chain I: L.413, T.414, H.438, M.490 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:L.413 Salt bridges: I:H.438, I:H.438 CPL.18: 7 residues within 4Å: Chain I: K.405, T.406, G.409, I.410, R.412, A.420, F.423 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:I.410 Salt bridges: I:R.412 CPL.22: 9 residues within 4Å: Chain M: I.410, L.413, T.414, V.415, G.417, H.438, G.442 Chain Q: G.10, T.13 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:I.410, M:L.413 Salt bridges: M:H.438, M:H.438 CPL.23: 7 residues within 4Å: Chain M: K.405, T.406, G.409, I.410, R.412, A.420, W.421 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:T.406 Salt bridges: M:R.412 CPL.24: 7 residues within 4Å: Chain N: T.414, V.415, G.417, H.438, M.490 Chain R: G.10, T.13 2 PLIP interactions: 2 interactions with chain N Salt bridges: N:H.438, N:H.438 CPL.25: 7 residues within 4Å: Chain N: K.405, T.406, G.409, I.410, R.412, W.421, F.423 3 PLIP interactions: 3 interactions with chain N Hydrophobic interactions: N:I.410 Salt bridges: N:K.405, N:R.412 CPL.26: 4 residues within 4Å: Chain O: L.413, T.414, H.438, M.490 3 PLIP interactions: 3 interactions with chain O Hydrophobic interactions: O:L.413 Salt bridges: O:H.438, O:H.438 CPL.27: 7 residues within 4Å: Chain O: K.405, T.406, G.409, I.410, R.412, A.420, F.423 2 PLIP interactions: 2 interactions with chain O Hydrophobic interactions: O:I.410 Salt bridges: O:R.412 CPL.31: 9 residues within 4Å: Chain S: I.410, L.413, T.414, V.415, G.417, H.438, G.442 Chain W: G.10, T.13 4 PLIP interactions: 4 interactions with chain S Hydrophobic interactions: S:I.410, S:L.413 Salt bridges: S:H.438, S:H.438 CPL.32: 7 residues within 4Å: Chain S: K.405, T.406, G.409, I.410, R.412, A.420, W.421 2 PLIP interactions: 2 interactions with chain S Hydrophobic interactions: S:T.406 Salt bridges: S:R.412 CPL.33: 7 residues within 4Å: Chain T: T.414, V.415, G.417, H.438, M.490 Chain X: G.10, T.13 2 PLIP interactions: 2 interactions with chain T Salt bridges: T:H.438, T:H.438 CPL.34: 7 residues within 4Å: Chain T: K.405, T.406, G.409, I.410, R.412, W.421, F.423 3 PLIP interactions: 3 interactions with chain T Hydrophobic interactions: T:I.410 Salt bridges: T:K.405, T:R.412 CPL.35: 4 residues within 4Å: Chain U: L.413, T.414, H.438, M.490 3 PLIP interactions: 3 interactions with chain U Hydrophobic interactions: U:L.413 Salt bridges: U:H.438, U:H.438 CPL.36: 7 residues within 4Å: Chain U: K.405, T.406, G.409, I.410, R.412, A.420, F.423 2 PLIP interactions: 2 interactions with chain U Hydrophobic interactions: U:I.410 Salt bridges: U:R.412 CPL.40: 9 residues within 4Å: Chain 2: G.10, T.13 Chain Y: I.410, L.413, T.414, V.415, G.417, H.438, G.442 4 PLIP interactions: 4 interactions with chain Y Hydrophobic interactions: Y:I.410, Y:L.413 Salt bridges: Y:H.438, Y:H.438 CPL.41: 7 residues within 4Å: Chain Y: K.405, T.406, G.409, I.410, R.412, A.420, W.421 2 PLIP interactions: 2 interactions with chain Y Hydrophobic interactions: Y:T.406 Salt bridges: Y:R.412 CPL.42: 7 residues within 4Å: Chain 3: G.10, T.13 Chain Z: T.414, V.415, G.417, H.438, M.490 2 PLIP interactions: 2 interactions with chain Z Salt bridges: Z:H.438, Z:H.438 CPL.43: 7 residues within 4Å: Chain Z: K.405, T.406, G.409, I.410, R.412, W.421, F.423 3 PLIP interactions: 3 interactions with chain Z Hydrophobic interactions: Z:I.410 Salt bridges: Z:K.405, Z:R.412 CPL.44: 4 residues within 4Å: Chain 0: L.413, T.414, H.438, M.490 3 PLIP interactions: 3 interactions with chain 0 Hydrophobic interactions: 0:L.413 Salt bridges: 0:H.438, 0:H.438 CPL.45: 7 residues within 4Å: Chain 0: K.405, T.406, G.409, I.410, R.412, A.420, F.423 2 PLIP interactions: 2 interactions with chain 0 Hydrophobic interactions: 0:I.410 Salt bridges: 0:R.412 CPL.49: 9 residues within 4Å: Chain 4: I.410, L.413, T.414, V.415, G.417, H.438, G.442 Chain 8: G.10, T.13 4 PLIP interactions: 4 interactions with chain 4 Hydrophobic interactions: 4:I.410, 4:L.413 Salt bridges: 4:H.438, 4:H.438 CPL.50: 7 residues within 4Å: Chain 4: K.405, T.406, G.409, I.410, R.412, A.420, W.421 2 PLIP interactions: 2 interactions with chain 4 Hydrophobic interactions: 4:T.406 Salt bridges: 4:R.412 CPL.51: 7 residues within 4Å: Chain 5: T.414, V.415, G.417, H.438, M.490 Chain 9: G.10, T.13 2 PLIP interactions: 2 interactions with chain 5 Salt bridges: 5:H.438, 5:H.438 CPL.52: 7 residues within 4Å: Chain 5: K.405, T.406, G.409, I.410, R.412, W.421, F.423 3 PLIP interactions: 3 interactions with chain 5 Hydrophobic interactions: 5:I.410 Salt bridges: 5:K.405, 5:R.412 CPL.53: 4 residues within 4Å: Chain 6: L.413, T.414, H.438, M.490 3 PLIP interactions: 3 interactions with chain 6 Hydrophobic interactions: 6:L.413 Salt bridges: 6:H.438, 6:H.438 CPL.54: 7 residues within 4Å: Chain 6: K.405, T.406, G.409, I.410, R.412, A.420, F.423 2 PLIP interactions: 2 interactions with chain 6 Hydrophobic interactions: 6:I.410 Salt bridges: 6:R.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pulkkinen, L.I.A. et al., Molecular Organisation of Tick-Borne Encephalitis Virus. Viruses (2022)

Release Date

2022-04-20

Peptides

Envelope protein E: ABCGHIMNOSTUYZ0456
Small envelope protein M: DEFJKLPQRVWX123789

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

G
A

H
B

I
C

M
A

N
B

O
C

S
A

T
B

U
C

Y
A

Z
B

0
C

4
A

5
B

6
C

D
D

E
E

F
F

J
D

K
E

L
F

P
D

Q
E

R
F

V
D

W
E

X
F

1
D

2
E

3
F

7
D

8
E

9
F

Envelope protein E

Small envelope protein M

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