SMTL ID : 3gzt.1 (1 other biounit)

VP7 recoated rotavirus DLP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-13-mer

Ligands

13 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain B: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain C: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain D: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain E: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain F: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain G: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain H: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain I: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain J: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain K: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain L: N.12 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain M: N.12 No protein-ligand interaction detected (PLIP)

30 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.14: 1 residues within 4Å: Chain A: D.244 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.244 CA.15: 1 residues within 4Å: Chain A: D.38 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.38 CA.16: 6 residues within 4Å: Chain A: Q.120, D.122, K.126, D.171, V.172, D.174 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.174, A:D.174 CA.17: 4 residues within 4Å: Chain A: G.149, T.157, F.158, E.159 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.157, A:E.159, A:E.159 CA.18: 7 residues within 4Å: Chain B: Q.120, D.122, K.126, D.171, V.172, D.174 Chain C: D.244 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:D.244, B:D.174, B:D.174 CA.19: 5 residues within 4Å: Chain B: G.149, T.157, F.158, E.159 Chain C: D.38 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Metal complexes: C:D.38, B:T.157, B:E.159, B:E.159 CA.20: 7 residues within 4Å: Chain C: Q.120, D.122, K.126, D.171, V.172, D.174 Chain D: D.244 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Metal complexes: D:D.244, C:D.174, C:D.174 CA.21: 5 residues within 4Å: Chain C: G.149, T.157, F.158, E.159 Chain D: D.38 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:T.157, C:E.159, C:E.159, D:D.38 CA.22: 7 residues within 4Å: Chain B: D.244 Chain D: Q.120, D.122, K.126, D.171, V.172, D.174 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Metal complexes: D:D.174, D:D.174, B:D.244 CA.23: 5 residues within 4Å: Chain B: D.38 Chain D: G.149, T.157, F.158, E.159 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Metal complexes: B:D.38, D:T.157, D:E.159, D:E.159 CA.24: 7 residues within 4Å: Chain E: Q.120, D.122, K.126, D.171, V.172, D.174 Chain F: D.244 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Metal complexes: E:D.174, E:D.174, F:D.244 CA.25: 5 residues within 4Å: Chain E: G.149, T.157, F.158, E.159 Chain F: D.38 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Metal complexes: E:T.157, E:E.159, E:E.159, F:D.38 CA.26: 7 residues within 4Å: Chain F: Q.120, D.122, K.126, D.171, V.172, D.174 Chain G: D.244 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Metal complexes: F:D.174, F:D.174, G:D.244 CA.27: 5 residues within 4Å: Chain F: G.149, T.157, F.158, E.159 Chain G: D.38 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Metal complexes: F:T.157, F:E.159, F:E.159, G:D.38 CA.28: 7 residues within 4Å: Chain E: D.244 Chain G: Q.120, D.122, K.126, D.171, V.172, D.174 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Metal complexes: E:D.244, G:D.174, G:D.174 CA.29: 5 residues within 4Å: Chain E: D.38 Chain G: G.149, T.157, F.158, E.159 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain G Metal complexes: E:D.38, G:T.157, G:E.159, G:E.159 CA.30: 7 residues within 4Å: Chain H: Q.120, D.122, K.126, D.171, V.172, D.174 Chain I: D.244 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain I Metal complexes: H:D.174, H:D.174, I:D.244 CA.31: 5 residues within 4Å: Chain H: G.149, T.157, F.158, E.159 Chain I: D.38 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Metal complexes: H:T.157, H:E.159, H:E.159, I:D.38 CA.32: 7 residues within 4Å: Chain I: Q.120, D.122, K.126, D.171, V.172, D.174 Chain J: D.244 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Metal complexes: I:D.174, I:D.174, J:D.244 CA.33: 5 residues within 4Å: Chain I: G.149, T.157, F.158, E.159 Chain J: D.38 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J Metal complexes: I:T.157, I:E.159, I:E.159, J:D.38 CA.34: 7 residues within 4Å: Chain H: D.244 Chain J: Q.120, D.122, K.126, D.171, V.172, D.174 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain H Metal complexes: J:D.174, J:D.174, H:D.244 CA.35: 5 residues within 4Å: Chain H: D.38 Chain J: G.149, T.157, F.158, E.159 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain H Metal complexes: J:T.157, J:E.159, J:E.159, H:D.38 CA.36: 7 residues within 4Å: Chain K: Q.120, D.122, K.126, D.171, V.172, D.174 Chain L: D.244 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K Metal complexes: L:D.244, K:D.174, K:D.174 CA.37: 5 residues within 4Å: Chain K: G.149, T.157, F.158, E.159 Chain L: D.38 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L Metal complexes: K:T.157, K:E.159, K:E.159, L:D.38 CA.38: 7 residues within 4Å: Chain L: Q.120, D.122, K.126, D.171, V.172, D.174 Chain M: D.244 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain M Metal complexes: L:D.174, L:D.174, M:D.244 CA.39: 5 residues within 4Å: Chain L: G.149, T.157, F.158, E.159 Chain M: D.38 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain L Metal complexes: M:D.38, L:T.157, L:E.159, L:E.159 CA.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.41: 7 residues within 4Å: Chain K: D.244 Chain M: Q.120, D.122, K.126, D.171, V.172, D.174 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain K Metal complexes: M:D.174, M:D.174, K:D.244 CA.42: 5 residues within 4Å: Chain K: D.38 Chain M: G.149, T.157, F.158, E.159 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain K Metal complexes: M:T.157, M:E.159, M:E.159, K:D.38 CA.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J.Z. et al., Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-07-14

Peptides

Outer capsid glycoprotein VP7: ABCDEFGHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

C
G

D
H

E
I

F
J

G
K

H
L

I
M

J
N

K
O

L
P

M
Q

Outer capsid glycoprotein VP7

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