SMTL ID : 4fte.2 (3 other biounits)

Crystal structure of the D75N mutant capsid of Flock House virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-15-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.221, G.273 Chain B: T.157, S.160, D.161, E.257 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.221, A:G.273, B:D.161 CA.2: 6 residues within 4Å: Chain A: D.249, E.251 Chain B: D.249, E.251 Chain C: D.249, E.251 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.249, C:D.249, C:E.251, A:D.249 CA.5: 6 residues within 4Å: Chain B: D.221, G.273 Chain C: T.157, S.160, D.161, E.257 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.161, B:G.273 CA.8: 5 residues within 4Å: Chain A: T.157, D.161, E.257 Chain C: D.221, G.273 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:D.161, C:G.273, H2O.9 CA.10: 6 residues within 4Å: Chain E: D.221, G.273 Chain F: T.157, S.160, D.161, E.257 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Metal complexes: E:D.221, E:G.273, F:D.161 CA.11: 6 residues within 4Å: Chain E: D.249, E.251 Chain F: D.249, E.251 Chain G: D.249, E.251 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 1 interactions with chain F Metal complexes: G:D.249, G:E.251, E:D.249, F:D.249 CA.14: 6 residues within 4Å: Chain F: D.221, G.273 Chain G: T.157, S.160, D.161, E.257 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Metal complexes: G:D.161, F:G.273 CA.17: 5 residues within 4Å: Chain E: T.157, D.161, E.257 Chain G: D.221, G.273 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: E:D.161, G:G.273, H2O.19 CA.19: 6 residues within 4Å: Chain I: D.221, G.273 Chain J: T.157, S.160, D.161, E.257 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Metal complexes: J:D.161, I:D.221, I:G.273 CA.20: 6 residues within 4Å: Chain I: D.249, E.251 Chain J: D.249, E.251 Chain K: D.249, E.251 4 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I, 1 interactions with chain J Metal complexes: K:D.249, K:E.251, I:D.249, J:D.249 CA.23: 6 residues within 4Å: Chain J: D.221, G.273 Chain K: T.157, S.160, D.161, E.257 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K Metal complexes: J:G.273, K:D.161 CA.26: 5 residues within 4Å: Chain I: T.157, D.161, E.257 Chain K: D.221, G.273 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: K:G.273, I:D.161, H2O.29 CA.28: 6 residues within 4Å: Chain M: D.221, G.273 Chain N: T.157, S.160, D.161, E.257 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain N Metal complexes: M:D.221, M:G.273, N:D.161 CA.29: 6 residues within 4Å: Chain M: D.249, E.251 Chain N: D.249, E.251 Chain O: D.249, E.251 4 PLIP interactions: 2 interactions with chain O, 1 interactions with chain M, 1 interactions with chain N Metal complexes: O:D.249, O:E.251, M:D.249, N:D.249 CA.32: 6 residues within 4Å: Chain N: D.221, G.273 Chain O: T.157, S.160, D.161, E.257 2 PLIP interactions: 1 interactions with chain N, 1 interactions with chain O Metal complexes: N:G.273, O:D.161 CA.35: 5 residues within 4Å: Chain M: T.157, D.161, E.257 Chain O: D.221, G.273 3 PLIP interactions: 1 interactions with chain M, 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: M:D.161, O:G.273, H2O.39 CA.37: 6 residues within 4Å: Chain Q: D.221, G.273 Chain R: T.157, S.160, D.161, E.257 3 PLIP interactions: 1 interactions with chain R, 2 interactions with chain Q Metal complexes: R:D.161, Q:D.221, Q:G.273 CA.38: 6 residues within 4Å: Chain Q: D.249, E.251 Chain R: D.249, E.251 Chain S: D.249, E.251 4 PLIP interactions: 2 interactions with chain S, 1 interactions with chain Q, 1 interactions with chain R Metal complexes: S:D.249, S:E.251, Q:D.249, R:D.249 CA.41: 6 residues within 4Å: Chain R: D.221, G.273 Chain S: T.157, S.160, D.161, E.257 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain S Metal complexes: R:G.273, S:D.161 CA.44: 5 residues within 4Å: Chain Q: T.157, D.161, E.257 Chain S: D.221, G.273 3 PLIP interactions: 1 interactions with chain S, 1 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: S:G.273, Q:D.161, H2O.49

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 9 residues within 4Å: Chain A: S.211, S.212, L.213 Chain B: S.211, S.212, L.213 Chain C: S.211, S.212, L.213 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:L.213, C:L.213, A:L.213, A:L.213 SO4.12: 9 residues within 4Å: Chain E: S.211, S.212, L.213 Chain F: S.211, S.212, L.213 Chain G: S.211, S.212, L.213 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G, 2 interactions with chain E Hydrogen bonds: F:L.213, G:L.213, E:L.213, E:L.213 SO4.21: 9 residues within 4Å: Chain I: S.211, S.212, L.213 Chain J: S.211, S.212, L.213 Chain K: S.211, S.212, L.213 4 PLIP interactions: 1 interactions with chain K, 2 interactions with chain I, 1 interactions with chain J Hydrogen bonds: K:L.213, I:L.213, I:L.213, J:L.213 SO4.30: 9 residues within 4Å: Chain M: S.211, S.212, L.213 Chain N: S.211, S.212, L.213 Chain O: S.211, S.212, L.213 4 PLIP interactions: 1 interactions with chain O, 2 interactions with chain M, 1 interactions with chain N Hydrogen bonds: O:L.213, M:L.213, M:L.213, N:L.213 SO4.39: 9 residues within 4Å: Chain Q: S.211, S.212, L.213 Chain R: S.211, S.212, L.213 Chain S: S.211, S.212, L.213 4 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain S, 1 interactions with chain R Hydrogen bonds: Q:L.213, Q:L.213, S:L.213, R:L.213

15 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 11 residues within 4Å: Chain A: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 Chain C: Q.201, F.202, P.203 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.260, A:T.261, A:A.265, A:E.283, C:Q.201 Salt bridges: A:E.283 EPE.7: 11 residues within 4Å: Chain A: Q.201, F.202, P.203 Chain B: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.260, B:T.261, B:A.265, B:E.283, A:Q.201 Salt bridges: B:E.283 EPE.9: 11 residues within 4Å: Chain B: Q.201, F.202, P.203 Chain C: S.156, G.258, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.260, C:T.261, C:A.265, C:E.283, B:Q.201 Salt bridges: C:E.283 EPE.13: 11 residues within 4Å: Chain E: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 Chain G: Q.201, F.202, P.203 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:Q.260, E:T.261, E:A.265, E:E.283, G:Q.201 Salt bridges: E:E.283 EPE.16: 11 residues within 4Å: Chain E: Q.201, F.202, P.203 Chain F: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.260, F:T.261, F:A.265, F:E.283, E:Q.201 Salt bridges: F:E.283 EPE.18: 11 residues within 4Å: Chain F: Q.201, F.202, P.203 Chain G: S.156, G.258, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:Q.260, G:T.261, G:A.265, G:E.283, F:Q.201 Salt bridges: G:E.283 EPE.22: 11 residues within 4Å: Chain I: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 Chain K: Q.201, F.202, P.203 6 PLIP interactions: 1 interactions with chain K, 5 interactions with chain I Hydrogen bonds: K:Q.201, I:Q.260, I:T.261, I:A.265, I:E.283 Salt bridges: I:E.283 EPE.25: 11 residues within 4Å: Chain I: Q.201, F.202, P.203 Chain J: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Q.260, J:T.261, J:A.265, J:E.283, I:Q.201 Salt bridges: J:E.283 EPE.27: 11 residues within 4Å: Chain J: Q.201, F.202, P.203 Chain K: S.156, G.258, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:Q.260, K:T.261, K:A.265, K:E.283, J:Q.201 Salt bridges: K:E.283 EPE.31: 11 residues within 4Å: Chain M: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 Chain O: Q.201, F.202, P.203 6 PLIP interactions: 5 interactions with chain M, 1 interactions with chain O Hydrogen bonds: M:Q.260, M:T.261, M:A.265, M:E.283, O:Q.201 Salt bridges: M:E.283 EPE.34: 11 residues within 4Å: Chain M: Q.201, F.202, P.203 Chain N: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 1 interactions with chain M, 5 interactions with chain N Hydrogen bonds: M:Q.201, N:Q.260, N:T.261, N:A.265, N:E.283 Salt bridges: N:E.283 EPE.36: 11 residues within 4Å: Chain N: Q.201, F.202, P.203 Chain O: S.156, G.258, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 1 interactions with chain N, 5 interactions with chain O Hydrogen bonds: N:Q.201, O:Q.260, O:T.261, O:A.265, O:E.283 Salt bridges: O:E.283 EPE.40: 11 residues within 4Å: Chain Q: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 Chain S: Q.201, F.202, P.203 6 PLIP interactions: 5 interactions with chain Q, 1 interactions with chain S Hydrogen bonds: Q:Q.260, Q:T.261, Q:A.265, Q:E.283, S:Q.201 Salt bridges: Q:E.283 EPE.43: 11 residues within 4Å: Chain Q: Q.201, F.202, P.203 Chain R: G.258, I.259, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 1 interactions with chain Q, 5 interactions with chain R Hydrogen bonds: Q:Q.201, R:Q.260, R:T.261, R:A.265, R:E.283 Salt bridges: R:E.283 EPE.45: 11 residues within 4Å: Chain R: Q.201, F.202, P.203 Chain S: S.156, G.258, Q.260, T.261, P.264, A.265, A.282, E.283 6 PLIP interactions: 5 interactions with chain S, 1 interactions with chain R Hydrogen bonds: S:Q.260, S:T.261, S:A.265, S:E.283, R:Q.201 Salt bridges: S:E.283

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

CL.6: 2 residues within 4Å: Chain B: S.102 Chain G: R.300 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain F: S.102 Chain K: R.300 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain J: S.102 Chain O: R.300 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain N: S.102 Chain S: R.300 Ligand excluded by PLIP CL.42: 2 residues within 4Å: Chain C: R.300 Chain R: S.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Speir, J.A. et al., Structural study of virus assembly intermediates reveals maturation event sequence and a staging position for externalized lytic peptides. to be published (2012)

Release Date

2012-08-01

Peptides

Capsid protein alpha: ABCEFGIJKMNOQRS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
A

F
B

G
C

I
A

J
B

K
C

M
A

N
B

O
C

Q
A

R
B

S
C

Capsid protein alpha

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