SMTL ID : 7cpi.1

His-Mediated Reversible Self-assembly of Ferritin Nanocage with Zn binding

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.23, E.58, H.61, V.106 Ligands: FE.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.23, A:E.58, A:H.61 FE.2: 6 residues within 4Å: Chain A: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.58, A:E.103, A:E.103 FE.5: 5 residues within 4Å: Chain B: E.23, E.58, H.61, V.106 Ligands: FE.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.23, B:E.58, B:H.61 FE.6: 6 residues within 4Å: Chain B: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.58, B:E.103, B:E.103 FE.7: 5 residues within 4Å: Chain C: E.23, E.58, H.61, V.106 Ligands: FE.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.23, C:E.58, C:H.61 FE.8: 6 residues within 4Å: Chain C: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.58, C:E.103, C:E.103 FE.10: 5 residues within 4Å: Chain D: E.23, E.58, H.61, V.106 Ligands: FE.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.23, D:E.58, D:H.61 FE.11: 6 residues within 4Å: Chain D: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.58, D:E.103, D:E.103 FE.14: 5 residues within 4Å: Chain E: E.23, E.58, H.61, V.106 Ligands: FE.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.23, E:E.58, E:H.61 FE.15: 6 residues within 4Å: Chain E: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.14 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.58, E:E.103, E:E.103 FE.16: 5 residues within 4Å: Chain F: E.23, E.58, H.61, V.106 Ligands: FE.17 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.23, F:E.58, F:H.61 FE.17: 6 residues within 4Å: Chain F: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.16 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.58, F:E.103, F:E.103 FE.19: 5 residues within 4Å: Chain G: E.23, E.58, H.61, V.106 Ligands: FE.20 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.23, G:E.58, G:H.61 FE.20: 6 residues within 4Å: Chain G: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.19 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.58, G:E.103, G:E.103 FE.23: 5 residues within 4Å: Chain H: E.23, E.58, H.61, V.106 Ligands: FE.24 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.23, H:E.58, H:H.61 FE.24: 6 residues within 4Å: Chain H: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.23 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.58, H:E.103, H:E.103 FE.25: 5 residues within 4Å: Chain I: E.23, E.58, H.61, V.106 Ligands: FE.26 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.23, I:E.58, I:H.61 FE.26: 6 residues within 4Å: Chain I: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.25 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.58, I:E.103, I:E.103 FE.28: 5 residues within 4Å: Chain J: E.23, E.58, H.61, V.106 Ligands: FE.29 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.23, J:E.58, J:H.61 FE.29: 6 residues within 4Å: Chain J: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.28 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.58, J:E.103, J:E.103 FE.32: 5 residues within 4Å: Chain K: E.23, E.58, H.61, V.106 Ligands: FE.33 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.23, K:E.58, K:H.61 FE.33: 6 residues within 4Å: Chain K: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.32 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.58, K:E.103, K:E.103 FE.34: 5 residues within 4Å: Chain L: E.23, E.58, H.61, V.106 Ligands: FE.35 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.23, L:E.58, L:H.61 FE.35: 6 residues within 4Å: Chain L: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.34 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.58, L:E.103, L:E.103 FE.37: 6 residues within 4Å: Chain M: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.38 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.23, M:E.58, M:H.61 FE.38: 6 residues within 4Å: Chain M: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.37 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.58, M:E.103, M:E.103 FE.40: 5 residues within 4Å: Chain N: E.23, E.58, H.61, V.106 Ligands: FE.41 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.23, N:E.58, N:H.61 FE.41: 7 residues within 4Å: Chain N: Y.30, E.58, H.61, E.103, Q.137, S.140 Ligands: FE.40 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.58, N:E.103, N:E.103 FE.43: 6 residues within 4Å: Chain O: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.44 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.23, O:E.58, O:H.61 FE.44: 7 residues within 4Å: Chain O: Y.30, E.58, H.61, E.103, V.106, Q.137 Ligands: FE.43 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.58, O:E.103, O:E.103 FE.47: 6 residues within 4Å: Chain P: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.48 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.23, P:E.58, P:H.61 FE.48: 6 residues within 4Å: Chain P: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.47 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.58, P:E.103, P:E.103 FE.50: 5 residues within 4Å: Chain Q: E.23, E.58, H.61, V.106 Ligands: FE.51 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.23, Q:E.58, Q:H.61 FE.51: 7 residues within 4Å: Chain Q: Y.30, E.58, H.61, E.103, Q.137, S.140 Ligands: FE.50 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.58, Q:E.103, Q:E.103 FE.53: 6 residues within 4Å: Chain R: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.54 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.23, R:E.58, R:H.61 FE.54: 7 residues within 4Å: Chain R: Y.30, E.58, H.61, E.103, V.106, Q.137 Ligands: FE.53 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.58, R:E.103, R:E.103 FE.57: 6 residues within 4Å: Chain S: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.58 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.23, S:E.58, S:H.61 FE.58: 6 residues within 4Å: Chain S: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.57 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.58, S:E.103, S:E.103 FE.60: 5 residues within 4Å: Chain T: E.23, E.58, H.61, V.106 Ligands: FE.61 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.23, T:E.58, T:H.61 FE.61: 7 residues within 4Å: Chain T: Y.30, E.58, H.61, E.103, Q.137, S.140 Ligands: FE.60 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.58, T:E.103, T:E.103 FE.63: 6 residues within 4Å: Chain U: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.64 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.23, U:E.58, U:H.61 FE.64: 7 residues within 4Å: Chain U: Y.30, E.58, H.61, E.103, V.106, Q.137 Ligands: FE.63 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.58, U:E.103, U:E.103 FE.67: 6 residues within 4Å: Chain V: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.68 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.23, V:E.58, V:H.61 FE.68: 6 residues within 4Å: Chain V: Y.30, E.58, H.61, E.103, Q.137 Ligands: FE.67 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.58, V:E.103, V:E.103 FE.70: 5 residues within 4Å: Chain W: E.23, E.58, H.61, V.106 Ligands: FE.71 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.23, W:E.58, W:H.61 FE.71: 7 residues within 4Å: Chain W: Y.30, E.58, H.61, E.103, Q.137, S.140 Ligands: FE.70 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.58, W:E.103, W:E.103 FE.73: 6 residues within 4Å: Chain X: E.23, E.58, H.61, V.106, Q.137 Ligands: FE.74 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.23, X:E.58, X:H.61 FE.74: 7 residues within 4Å: Chain X: Y.30, E.58, H.61, E.103, V.106, Q.137 Ligands: FE.73 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.58, X:E.103, X:E.103

28 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.3: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: ZN.12, ZN.21, ZN.30 No protein-ligand interaction detected (PLIP) ZN.4: 3 residues within 4Å: Ligands: ZN.13, ZN.22, ZN.31 No protein-ligand interaction detected (PLIP) ZN.9: 5 residues within 4Å: Chain C: D.131 Chain J: K.127, D.131 Chain K: K.127, D.131 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.131 ZN.12: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: ZN.3, ZN.21, ZN.30 No protein-ligand interaction detected (PLIP) ZN.13: 3 residues within 4Å: Ligands: ZN.4, ZN.22, ZN.31 No protein-ligand interaction detected (PLIP) ZN.18: 5 residues within 4Å: Chain F: D.131 Chain G: K.127, D.131 Chain H: K.127, D.131 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.131 ZN.21: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: ZN.3, ZN.12, ZN.30 No protein-ligand interaction detected (PLIP) ZN.22: 3 residues within 4Å: Ligands: ZN.4, ZN.13, ZN.31 No protein-ligand interaction detected (PLIP) ZN.27: 5 residues within 4Å: Chain A: K.127, D.131 Chain B: K.127, D.131 Chain I: D.131 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.131 ZN.30: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: ZN.3, ZN.12, ZN.21 No protein-ligand interaction detected (PLIP) ZN.31: 3 residues within 4Å: Ligands: ZN.4, ZN.13, ZN.22 No protein-ligand interaction detected (PLIP) ZN.36: 5 residues within 4Å: Chain D: K.127, D.131 Chain E: K.127, D.131 Chain L: D.131 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.131 ZN.39: 1 residues within 4Å: Chain E: H.157 No protein-ligand interaction detected (PLIP) ZN.42: 4 residues within 4Å: Chain E: H.159 Chain F: H.159 Chain M: H.159 Chain N: H.159 6 PLIP interactions: 1 interactions with chain M, 1 interactions with chain N, 1 interactions with chain F, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: M:H.159, N:H.159, F:H.159, E:H.159, H2O.2, H2O.2 ZN.45: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: ZN.55, ZN.65, ZN.75 5 PLIP interactions: 1 interactions with chain O, 1 interactions with chain U, 1 interactions with chain R, 1 interactions with chain X, 1 Ligand-Water interactions Metal complexes: O:H.159, U:H.159, R:H.159, X:H.159, H2O.2 ZN.46: 3 residues within 4Å: Ligands: ZN.56, ZN.66, ZN.76 No protein-ligand interaction detected (PLIP) ZN.49: 1 residues within 4Å: Chain B: H.157 No protein-ligand interaction detected (PLIP) ZN.52: 4 residues within 4Å: Chain B: H.159 Chain C: H.159 Chain P: H.159 Chain Q: H.159 6 PLIP interactions: 1 interactions with chain P, 1 interactions with chain C, 1 interactions with chain Q, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: P:H.159, C:H.159, Q:H.159, B:H.159, H2O.2, H2O.2 ZN.55: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: ZN.45, ZN.65, ZN.75 5 PLIP interactions: 1 interactions with chain R, 1 interactions with chain O, 1 interactions with chain U, 1 interactions with chain X, 1 Ligand-Water interactions Metal complexes: R:H.159, O:H.159, U:H.159, X:H.159, H2O.2 ZN.56: 3 residues within 4Å: Ligands: ZN.46, ZN.66, ZN.76 No protein-ligand interaction detected (PLIP) ZN.59: 1 residues within 4Å: Chain K: H.157 No protein-ligand interaction detected (PLIP) ZN.62: 4 residues within 4Å: Chain K: H.159 Chain L: H.159 Chain S: H.159 Chain T: H.159 6 PLIP interactions: 1 interactions with chain L, 1 interactions with chain T, 1 interactions with chain K, 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: L:H.159, T:H.159, K:H.159, S:H.159, H2O.2, H2O.3 ZN.65: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: ZN.45, ZN.55, ZN.75 5 PLIP interactions: 1 interactions with chain O, 1 interactions with chain U, 1 interactions with chain X, 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: O:H.159, U:H.159, X:H.159, R:H.159, H2O.2 ZN.66: 3 residues within 4Å: Ligands: ZN.46, ZN.56, ZN.76 No protein-ligand interaction detected (PLIP) ZN.69: 1 residues within 4Å: Chain H: H.157 No protein-ligand interaction detected (PLIP) ZN.72: 4 residues within 4Å: Chain H: H.159 Chain I: H.159 Chain V: H.159 Chain W: H.159 6 PLIP interactions: 1 interactions with chain H, 1 interactions with chain W, 1 interactions with chain V, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: H:H.159, W:H.159, V:H.159, I:H.159, H2O.3, H2O.3 ZN.75: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: ZN.45, ZN.55, ZN.65 5 PLIP interactions: 1 interactions with chain O, 1 interactions with chain U, 1 interactions with chain X, 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: O:H.159, U:H.159, X:H.159, R:H.159, H2O.2 ZN.76: 3 residues within 4Å: Ligands: ZN.46, ZN.56, ZN.66 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, C. et al., His-Mediated Reversible Self-Assembly of Ferritin Nanocages through Two Different Switches for Encapsulation of Cargo Molecules. Acs Nano (2020)

Release Date

2021-06-16

Peptides

Ferritin: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
A

E
B

F
F

G
A

H
B

I
F

J
A

K
B

L
F

M
E

N
C

O
D

P
E

Q
C

R
D

S
E

T
C

U
D

V
E

W
C

X
D

Ferritin

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