SMTL ID : 7ke5.1

Heavy chain ferritin with N-terminal EBNA1 epitope

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-24-mer

Ligands

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

TRS.1: 5 residues within 4Å: Chain A: L.55, S.58 Chain B: S.58, R.90, I.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.58 TRS.5: 3 residues within 4Å: Chain C: S.58, R.90 Chain D: L.55 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.90, C:R.90 TRS.10: 9 residues within 4Å: Chain E: L.55, S.58, Y.59, R.90, I.112 Chain F: L.55, S.58, R.90, I.112 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.90, F:R.90, E:R.90, E:R.90 TRS.15: 7 residues within 4Å: Chain G: L.55, R.90, I.112 Chain H: L.55, S.58, Y.59, I.112 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.90, H:S.58, H:S.58 TRS.17: 5 residues within 4Å: Chain I: L.55, S.58, Y.59, R.90, I.112 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:L.55, I:R.90, I:R.90, J:S.58 TRS.21: 10 residues within 4Å: Chain K: L.55, S.58, Y.59, R.90, I.112 Chain L: L.55, S.58, Y.59, R.90, I.112 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:R.90, L:S.58, L:R.90, L:R.90 TRS.23: 5 residues within 4Å: Chain M: L.55, S.58 Chain N: S.58, R.90, I.112 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:S.58 TRS.27: 3 residues within 4Å: Chain O: S.58, R.90 Chain P: L.55 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:R.90, O:R.90 TRS.32: 9 residues within 4Å: Chain Q: L.55, S.58, Y.59, R.90, I.112 Chain R: L.55, S.58, R.90, I.112 4 PLIP interactions: 2 interactions with chain Q, 2 interactions with chain R Hydrogen bonds: Q:R.90, Q:R.90, R:R.90, R:R.90 TRS.37: 7 residues within 4Å: Chain S: L.55, R.90, I.112 Chain T: L.55, S.58, Y.59, I.112 3 PLIP interactions: 2 interactions with chain T, 1 interactions with chain S Hydrogen bonds: T:S.58, T:S.58, S:R.90 TRS.39: 5 residues within 4Å: Chain U: L.55, S.58, Y.59, R.90, I.112 4 PLIP interactions: 3 interactions with chain U, 1 interactions with chain V Hydrogen bonds: U:L.55, U:R.90, U:R.90, V:S.58 TRS.43: 10 residues within 4Å: Chain W: L.55, S.58, Y.59, R.90, I.112 Chain X: L.55, S.58, Y.59, R.90, I.112 4 PLIP interactions: 1 interactions with chain W, 3 interactions with chain X Hydrogen bonds: W:R.90, X:S.58, X:R.90, X:R.90

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

FE.2: 5 residues within 4Å: Chain A: E.54, E.89, H.92, V.137, Q.168 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.54, A:E.54, A:E.89, A:E.89, A:H.92 FE.3: 6 residues within 4Å: Chain A: D.158, E.161 Chain H: D.158, E.161 Chain R: D.158, E.161 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain A, 1 interactions with chain R Metal complexes: H:D.158, H:E.161, A:D.158, A:E.161, R:E.161 FE.4: 4 residues within 4Å: Chain B: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.54, B:E.89, B:E.89, B:H.92 FE.6: 5 residues within 4Å: Chain C: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.54, C:E.54, C:E.89, C:H.92 FE.7: 6 residues within 4Å: Chain C: D.158, E.161 Chain J: D.158, E.161 Chain L: D.158, E.161 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C, 2 interactions with chain J Metal complexes: L:D.158, L:E.161, C:E.161, J:D.158, J:E.161 FE.8: 5 residues within 4Å: Chain D: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.54, D:E.54, D:E.89, D:H.92 FE.9: 6 residues within 4Å: Chain D: D.158, E.161 Chain G: D.158, E.161 Chain W: D.158, E.161 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain W, 1 interactions with chain G Metal complexes: D:D.158, D:E.161, W:D.158, W:E.161, G:E.161 FE.11: 5 residues within 4Å: Chain E: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.54, E:E.89, E:E.89, E:H.92 FE.12: 6 residues within 4Å: Chain B: D.158, E.161 Chain E: D.158, E.161 Chain I: D.158, E.161 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B, 2 interactions with chain I Metal complexes: E:D.158, E:E.161, B:E.161, I:D.158, I:E.161 FE.13: 4 residues within 4Å: Chain F: E.54, E.89, H.92, Q.168 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.54, F:E.89, F:H.92 FE.14: 5 residues within 4Å: Chain G: E.54, E.89, H.92, V.137, Q.168 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.54, G:E.89, G:H.92 FE.16: 5 residues within 4Å: Chain H: E.54, E.89, H.92, V.137, Q.168 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.54, H:E.54, H:E.89, H:E.89, H:H.92 FE.18: 4 residues within 4Å: Chain I: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.54, I:E.54, I:E.89, I:H.92 FE.19: 4 residues within 4Å: Chain J: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.54, J:E.54, J:E.89, J:H.92 FE.20: 4 residues within 4Å: Chain K: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.54, K:E.54, K:E.89, K:H.92 FE.22: 5 residues within 4Å: Chain L: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.54, L:E.54, L:E.89, L:H.92 FE.24: 5 residues within 4Å: Chain M: E.54, E.89, H.92, V.137, Q.168 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.54, M:E.54, M:E.89, M:E.89, M:H.92 FE.25: 6 residues within 4Å: Chain F: D.158, E.161 Chain M: D.158, E.161 Chain T: D.158, E.161 5 PLIP interactions: 2 interactions with chain M, 1 interactions with chain F, 2 interactions with chain T Metal complexes: M:D.158, M:E.161, F:E.161, T:D.158, T:E.161 FE.26: 4 residues within 4Å: Chain N: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.54, N:E.89, N:E.89, N:H.92 FE.28: 5 residues within 4Å: Chain O: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.54, O:E.54, O:E.89, O:H.92 FE.29: 6 residues within 4Å: Chain O: D.158, E.161 Chain V: D.158, E.161 Chain X: D.158, E.161 5 PLIP interactions: 1 interactions with chain O, 2 interactions with chain V, 2 interactions with chain X Metal complexes: O:E.161, V:D.158, V:E.161, X:D.158, X:E.161 FE.30: 5 residues within 4Å: Chain P: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.54, P:E.54, P:E.89, P:H.92 FE.31: 6 residues within 4Å: Chain K: D.158, E.161 Chain P: D.158, E.161 Chain S: D.158, E.161 5 PLIP interactions: 2 interactions with chain K, 2 interactions with chain P, 1 interactions with chain S Metal complexes: K:D.158, K:E.161, P:D.158, P:E.161, S:E.161 FE.33: 5 residues within 4Å: Chain Q: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.54, Q:E.89, Q:E.89, Q:H.92 FE.34: 6 residues within 4Å: Chain N: D.158, E.161 Chain Q: D.158, E.161 Chain U: D.158, E.161 5 PLIP interactions: 1 interactions with chain N, 2 interactions with chain U, 2 interactions with chain Q Metal complexes: N:E.161, U:D.158, U:E.161, Q:D.158, Q:E.161 FE.35: 4 residues within 4Å: Chain R: E.54, E.89, H.92, Q.168 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.54, R:E.89, R:H.92 FE.36: 5 residues within 4Å: Chain S: E.54, E.89, H.92, V.137, Q.168 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.54, S:E.89, S:H.92 FE.38: 5 residues within 4Å: Chain T: E.54, E.89, H.92, V.137, Q.168 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.54, T:E.54, T:E.89, T:E.89, T:H.92 FE.40: 4 residues within 4Å: Chain U: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.54, U:E.54, U:E.89, U:H.92 FE.41: 4 residues within 4Å: Chain V: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:E.54, V:E.54, V:E.89, V:H.92 FE.42: 4 residues within 4Å: Chain W: E.54, E.89, H.92, Q.168 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.54, W:E.54, W:E.89, W:H.92 FE.44: 5 residues within 4Å: Chain X: E.54, E.89, H.92, V.137, Q.168 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:E.54, X:E.54, X:E.89, X:H.92

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

Epstein-Barr nuclear antigen 1,Ferritin heavy chain: 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

Epstein-Barr nuclear antigen 1,Ferritin heavy chain