SMTL ID : 7ke3.1

Heavy chain ferritin with C-terminal EBNA1 epitope

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-24-mer

Ligands

12 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 7 residues within 4Å: Chain A: L.29, S.32, R.64 Chain B: L.29, S.32, Y.33, R.64 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.32, B:R.64, A:R.64 TRS.6: 7 residues within 4Å: Chain C: L.29, S.32, Y.33, R.64 Chain D: L.29, S.32, I.86 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.29, C:S.32, C:S.32, C:R.64, D:S.32 TRS.15: 10 residues within 4Å: Chain E: L.29, S.32, Y.33, L.36, R.64, I.86 Chain F: L.29, S.32, R.64, I.86 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:L.29, F:R.64, F:R.64 TRS.19: 7 residues within 4Å: Chain G: L.29, R.64, I.86 Chain H: L.29, S.32, Y.33, R.64 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.32, H:S.32, H:R.64 TRS.21: 7 residues within 4Å: Chain I: L.29, S.32, R.64, I.86 Chain J: S.32, Y.33, R.64 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:S.32, J:S.32, J:R.64, I:R.64, I:R.64 TRS.24: 8 residues within 4Å: Chain K: L.29, S.32, Y.33, R.64 Chain L: L.29, S.32, R.64, I.86 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:S.32, K:L.29, K:S.32 TRS.27: 7 residues within 4Å: Chain M: L.29, S.32, R.64 Chain N: L.29, S.32, Y.33, R.64 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:R.64, N:S.32, N:R.64 TRS.32: 7 residues within 4Å: Chain O: L.29, S.32, Y.33, R.64 Chain P: L.29, S.32, I.86 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain P Hydrogen bonds: O:L.29, O:S.32, O:S.32, O:R.64, P:S.32 TRS.41: 10 residues within 4Å: Chain Q: L.29, S.32, Y.33, L.36, R.64, I.86 Chain R: L.29, S.32, R.64, I.86 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain R Hydrogen bonds: Q:L.29, R:R.64, R:R.64 TRS.45: 7 residues within 4Å: Chain S: L.29, R.64, I.86 Chain T: L.29, S.32, Y.33, R.64 3 PLIP interactions: 3 interactions with chain T Hydrogen bonds: T:S.32, T:S.32, T:R.64 TRS.47: 7 residues within 4Å: Chain U: L.29, S.32, R.64, I.86 Chain V: S.32, Y.33, R.64 5 PLIP interactions: 3 interactions with chain V, 2 interactions with chain U Hydrogen bonds: V:S.32, V:S.32, V:R.64, U:R.64, U:R.64 TRS.50: 8 residues within 4Å: Chain W: L.29, S.32, Y.33, R.64 Chain X: L.29, S.32, R.64, I.86 3 PLIP interactions: 2 interactions with chain W, 1 interactions with chain X Hydrogen bonds: W:L.29, W:S.32, X:S.32

40 x FE: FE (III) ION(Non-covalent)

FE.2: 4 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.28, A:E.63, A:H.66 FE.3: 6 residues within 4Å: Chain A: D.132, E.135 Chain H: D.132, E.135 Chain R: D.132, E.135 5 PLIP interactions: 2 interactions with chain R, 2 interactions with chain H, 1 interactions with chain A Metal complexes: R:D.132, R:E.135, H:D.132, H:E.135, A:D.132 FE.4: 4 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.28, B:E.63, B:E.63, B:H.66 FE.5: 4 residues within 4Å: Chain B: H.174 Chain D: H.174 Chain H: H.174 Chain J: H.174 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain H, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: J:H.174, D:H.174, H:H.174, B:H.174, H2O.9 FE.7: 6 residues within 4Å: Chain C: D.132, E.135 Chain J: D.132, E.135 Chain L: D.132, E.135 4 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C, 1 interactions with chain J Metal complexes: L:D.132, L:E.135, C:E.135, J:D.132 FE.8: 4 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.28, C:E.63, C:H.66 FE.9: 5 residues within 4Å: Chain C: H.174 Chain K: H.174 Chain O: H.174 Chain W: H.174 Ligands: FE.35 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain W, 1 interactions with chain C, 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: K:H.174, W:H.174, C:H.174, O:H.174, H2O.7 FE.10: 6 residues within 4Å: Chain D: D.132, E.135 Chain G: D.132, E.135 Chain W: D.132, E.135 5 PLIP interactions: 2 interactions with chain G, 2 interactions with chain W, 1 interactions with chain D Metal complexes: G:D.132, G:E.135, W:D.132, W:E.135, D:D.132 FE.11: 4 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.28, D:E.63, D:H.66 FE.12: 5 residues within 4Å: Chain A: H.174 Chain E: H.174 Chain M: H.174 Chain Q: H.174 Ligands: FE.38 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain A, 1 interactions with chain Q, 1 interactions with chain E Metal complexes: M:H.174, A:H.174, Q:H.174, E:H.174 FE.13: 4 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.28, E:E.63, E:H.66 FE.14: 6 residues within 4Å: Chain B: D.132, E.135 Chain E: D.132, E.135 Chain I: D.132, E.135 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain I, 1 interactions with chain E Metal complexes: B:D.132, B:E.135, I:D.132, I:E.135, E:D.132 FE.16: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.28, F:E.63, F:H.66 FE.17: 4 residues within 4Å: Chain G: H.174 Chain R: H.174 Chain U: H.174 Chain X: H.174 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain U, 1 interactions with chain X, 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: G:H.174, U:H.174, X:H.174, R:H.174, H2O.41 FE.18: 4 residues within 4Å: Chain G: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.28, G:E.63, G:H.66 FE.20: 4 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.28, H:E.63, H:H.66 FE.22: 4 residues within 4Å: Chain I: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.28, I:E.63, I:H.66 FE.23: 4 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.28, J:E.63, J:H.66 FE.25: 4 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.28, K:E.63, K:H.66 FE.26: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.28, L:E.63, L:H.66 FE.28: 4 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.28, M:E.63, M:H.66 FE.29: 6 residues within 4Å: Chain F: D.132, E.135 Chain M: D.132, E.135 Chain T: D.132, E.135 5 PLIP interactions: 1 interactions with chain M, 2 interactions with chain F, 2 interactions with chain T Metal complexes: M:D.132, F:D.132, F:E.135, T:D.132, T:E.135 FE.30: 4 residues within 4Å: Chain N: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.28, N:E.63, N:E.63, N:H.66 FE.31: 4 residues within 4Å: Chain N: H.174 Chain P: H.174 Chain T: H.174 Chain V: H.174 5 PLIP interactions: 1 interactions with chain P, 1 interactions with chain T, 1 interactions with chain V, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: P:H.174, T:H.174, V:H.174, N:H.174, H2O.36 FE.33: 6 residues within 4Å: Chain O: D.132, E.135 Chain V: D.132, E.135 Chain X: D.132, E.135 4 PLIP interactions: 2 interactions with chain X, 1 interactions with chain V, 1 interactions with chain O Metal complexes: X:D.132, X:E.135, V:D.132, O:E.135 FE.34: 4 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.28, O:E.63, O:H.66 FE.35: 5 residues within 4Å: Chain C: H.174 Chain K: H.174 Chain O: H.174 Chain W: H.174 Ligands: FE.9 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain O, 1 interactions with chain K, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: C:H.174, O:H.174, K:H.174, W:H.174, H2O.7 FE.36: 6 residues within 4Å: Chain K: D.132, E.135 Chain P: D.132, E.135 Chain S: D.132, E.135 5 PLIP interactions: 1 interactions with chain P, 2 interactions with chain S, 2 interactions with chain K Metal complexes: P:D.132, S:D.132, S:E.135, K:D.132, K:E.135 FE.37: 4 residues within 4Å: Chain P: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.28, P:E.63, P:H.66 FE.38: 5 residues within 4Å: Chain A: H.174 Chain E: H.174 Chain M: H.174 Chain Q: H.174 Ligands: FE.12 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain A, 1 interactions with chain Q, 1 interactions with chain E Metal complexes: M:H.174, A:H.174, Q:H.174, E:H.174 FE.39: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.28, Q:E.63, Q:H.66 FE.40: 6 residues within 4Å: Chain N: D.132, E.135 Chain Q: D.132, E.135 Chain U: D.132, E.135 5 PLIP interactions: 2 interactions with chain U, 2 interactions with chain N, 1 interactions with chain Q Metal complexes: U:D.132, U:E.135, N:D.132, N:E.135, Q:D.132 FE.42: 4 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.28, R:E.63, R:H.66 FE.43: 4 residues within 4Å: Chain F: H.174 Chain I: H.174 Chain L: H.174 Chain S: H.174 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain S, 1 interactions with chain F, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: I:H.174, S:H.174, F:H.174, L:H.174, H2O.14 FE.44: 4 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.28, S:E.63, S:H.66 FE.46: 4 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.28, T:E.63, T:H.66 FE.48: 4 residues within 4Å: Chain U: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.28, U:E.63, U:H.66 FE.49: 4 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.28, V:E.63, V:H.66 FE.51: 4 residues within 4Å: Chain W: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.28, W:E.63, W:H.66 FE.52: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.28, X:E.63, X:H.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qu, Y. et al., Immunogenicity study of engineered ferritins with C- and N-terminus insertion of Epstein-Barr nuclear antigen 1 epitope. Vaccine (2021)

Release Date

2021-09-01

Peptides

Ferritin heavy chain,Epstein-Barr nuclear antigen 1: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
A

N
B

O
C

P
D

Q
E

R
F

S
G

T
H

U
I

V
J

W
K

X
L

Ferritin heavy chain,Epstein-Barr nuclear antigen 1