SMTL ID : 7cpc.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-24-mer

Ligands

24 x NI: NICKEL (II) ION(Non-covalent)(Non-functional Binders)

NI.1: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: NI.7, NI.13, NI.19 Ligand excluded by PLIP NI.2: 3 residues within 4Å: Ligands: NI.8, NI.14, NI.20 Ligand excluded by PLIP NI.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NI.7: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: NI.1, NI.13, NI.19 Ligand excluded by PLIP NI.8: 3 residues within 4Å: Ligands: NI.2, NI.14, NI.20 Ligand excluded by PLIP NI.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NI.13: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: NI.1, NI.7, NI.19 Ligand excluded by PLIP NI.14: 3 residues within 4Å: Ligands: NI.2, NI.8, NI.20 Ligand excluded by PLIP NI.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NI.19: 7 residues within 4Å: Chain A: H.159 Chain D: H.159 Chain G: H.159 Chain J: H.159 Ligands: NI.1, NI.7, NI.13 Ligand excluded by PLIP NI.20: 3 residues within 4Å: Ligands: NI.2, NI.8, NI.14 Ligand excluded by PLIP NI.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NI.25: 4 residues within 4Å: Chain E: H.159 Chain F: H.159 Chain M: H.159 Chain N: H.159 Ligand excluded by PLIP NI.28: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: NI.34, NI.40, NI.46 Ligand excluded by PLIP NI.29: 3 residues within 4Å: Ligands: NI.35, NI.41, NI.47 Ligand excluded by PLIP NI.31: 4 residues within 4Å: Chain B: H.159 Chain C: H.159 Chain P: H.159 Chain Q: H.159 Ligand excluded by PLIP NI.34: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: NI.28, NI.40, NI.46 Ligand excluded by PLIP NI.35: 3 residues within 4Å: Ligands: NI.29, NI.41, NI.47 Ligand excluded by PLIP NI.37: 4 residues within 4Å: Chain K: H.159 Chain L: H.159 Chain S: H.159 Chain T: H.159 Ligand excluded by PLIP NI.40: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: NI.28, NI.34, NI.46 Ligand excluded by PLIP NI.41: 3 residues within 4Å: Ligands: NI.29, NI.35, NI.47 Ligand excluded by PLIP NI.43: 4 residues within 4Å: Chain H: H.159 Chain I: H.159 Chain V: H.159 Chain W: H.159 Ligand excluded by PLIP NI.46: 7 residues within 4Å: Chain O: H.159 Chain R: H.159 Chain U: H.159 Chain X: H.159 Ligands: NI.28, NI.34, NI.40 Ligand excluded by PLIP NI.47: 3 residues within 4Å: Ligands: NI.29, NI.35, NI.41 Ligand excluded by PLIP

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

FE.3: 3 residues within 4Å: Chain A: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.23, A:E.58, A:E.58 FE.5: 4 residues within 4Å: Chain B: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.23, B:E.58, B:H.61 FE.6: 5 residues within 4Å: Chain C: E.23, E.58, H.61, V.106, Q.137 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.23, C:E.58, C:E.58 FE.9: 3 residues within 4Å: Chain D: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.23, D:E.58, D:E.58 FE.11: 4 residues within 4Å: Chain E: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.23, E:E.58, E:H.61 FE.12: 5 residues within 4Å: Chain F: E.23, E.58, H.61, V.106, Q.137 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.23, F:E.58, F:E.58 FE.15: 3 residues within 4Å: Chain G: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.23, G:E.58, G:E.58 FE.17: 4 residues within 4Å: Chain H: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.23, H:E.58, H:H.61 FE.18: 5 residues within 4Å: Chain I: E.23, E.58, H.61, V.106, Q.137 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.23, I:E.58, I:E.58 FE.21: 3 residues within 4Å: Chain J: E.23, E.58, H.61 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.23, J:E.58, J:E.58 FE.23: 4 residues within 4Å: Chain K: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.23, K:E.58, K:H.61 FE.24: 5 residues within 4Å: Chain L: E.23, E.58, H.61, V.106, Q.137 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.23, L:E.58, L:E.58 FE.26: 4 residues within 4Å: Chain M: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.23, M:E.58, M:H.61 FE.27: 4 residues within 4Å: Chain N: E.23, E.58, H.61, Q.137 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.23, N:E.58, N:E.58, N:H.61 FE.30: 3 residues within 4Å: Chain O: E.23, E.58, H.61 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:E.23, O:E.58 FE.32: 4 residues within 4Å: Chain P: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.23, P:E.58, P:H.61 FE.33: 4 residues within 4Å: Chain Q: E.23, E.58, H.61, Q.137 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:E.23, Q:E.58, Q:E.58, Q:H.61 FE.36: 3 residues within 4Å: Chain R: E.23, E.58, H.61 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:E.23, R:E.58 FE.38: 4 residues within 4Å: Chain S: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.23, S:E.58, S:H.61 FE.39: 4 residues within 4Å: Chain T: E.23, E.58, H.61, Q.137 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:E.23, T:E.58, T:E.58, T:H.61 FE.42: 3 residues within 4Å: Chain U: E.23, E.58, H.61 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:E.23, U:E.58 FE.44: 4 residues within 4Å: Chain V: E.23, E.58, H.61, Q.137 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.23, V:E.58, V:H.61 FE.45: 4 residues within 4Å: Chain W: E.23, E.58, H.61, Q.137 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.23, W:E.58, W:E.58, W:H.61 FE.48: 3 residues within 4Å: Chain X: E.23, E.58, H.61 2 PLIP interactions: 2 interactions with chain X Metal complexes: X:E.23, X:E.58

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
C

C
F

D
A

E
C

F
F

G
A

H
C

I
F

J
A

K
C

L
F

M
B

N
D

O
E

P
B

Q
D

R
E

S
B

T
D

U
E

V
B

W
D

X
E

Ferritin

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