SMTL ID : 1f2n.3 (3 other biounits)

RICE YELLOW MOTTLE VIRUS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-18-mer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.126, D.129 Chain B: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.126, A:D.129, B:V.182, B:T.238 CA.2: 5 residues within 4Å: Chain B: D.126, D.129 Chain C: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Metal complexes: B:D.126, B:D.129, C:V.182, C:T.238 CA.3: 5 residues within 4Å: Chain A: V.182, N.237, T.238 Chain C: D.126, D.129 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Metal complexes: C:D.126, C:D.129, A:V.182, A:T.238 CA.4: 5 residues within 4Å: Chain D: D.126, D.129 Chain E: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Metal complexes: D:D.126, D:D.129, E:V.182, E:T.238 CA.5: 5 residues within 4Å: Chain E: D.126, D.129 Chain F: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Metal complexes: F:V.182, F:T.238, E:D.126, E:D.129 CA.6: 5 residues within 4Å: Chain D: V.182, N.237, T.238 Chain F: D.126, D.129 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Metal complexes: F:D.126, F:D.129, D:V.182, D:T.238 CA.7: 5 residues within 4Å: Chain G: D.126, D.129 Chain H: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H Metal complexes: G:D.126, G:D.129, H:V.182, H:T.238 CA.8: 5 residues within 4Å: Chain H: D.126, D.129 Chain I: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain I Metal complexes: H:D.126, H:D.129, I:V.182, I:T.238 CA.9: 5 residues within 4Å: Chain G: V.182, N.237, T.238 Chain I: D.126, D.129 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain I Metal complexes: G:V.182, G:T.238, I:D.126, I:D.129 CA.10: 5 residues within 4Å: Chain J: D.126, D.129 Chain K: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain K Metal complexes: J:D.126, J:D.129, K:V.182, K:T.238 CA.11: 5 residues within 4Å: Chain K: D.126, D.129 Chain L: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain L Metal complexes: K:D.126, K:D.129, L:V.182, L:T.238 CA.12: 5 residues within 4Å: Chain J: V.182, N.237, T.238 Chain L: D.126, D.129 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain L Metal complexes: J:V.182, J:T.238, L:D.126, L:D.129 CA.13: 5 residues within 4Å: Chain M: D.126, D.129 Chain N: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain N Metal complexes: M:D.126, M:D.129, N:V.182, N:T.238 CA.14: 5 residues within 4Å: Chain N: D.126, D.129 Chain O: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain O Metal complexes: N:D.126, N:D.129, O:V.182, O:T.238 CA.15: 5 residues within 4Å: Chain M: V.182, N.237, T.238 Chain O: D.126, D.129 4 PLIP interactions: 2 interactions with chain M, 2 interactions with chain O Metal complexes: M:V.182, M:T.238, O:D.126, O:D.129 CA.16: 5 residues within 4Å: Chain P: D.126, D.129 Chain Q: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain Q Metal complexes: P:D.126, P:D.129, Q:V.182, Q:T.238 CA.17: 5 residues within 4Å: Chain Q: D.126, D.129 Chain R: V.182, N.237, T.238 4 PLIP interactions: 2 interactions with chain R, 2 interactions with chain Q Metal complexes: R:V.182, R:T.238, Q:D.126, Q:D.129 CA.18: 5 residues within 4Å: Chain P: V.182, N.237, T.238 Chain R: D.126, D.129 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain R Metal complexes: P:V.182, P:T.238, R:D.126, R:D.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qu, C. et al., 3D domain swapping modulates the stability of members of an icosahedral virus group. Structure Fold.Des. (2000)

Release Date

2000-11-01

Peptides

CAPSID PROTEIN: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

CAPSID PROTEIN

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