SMTL ID : 6sht.1

Molecular structure of mouse apoferritin resolved at 2.7 Angstroms with the Glacios cryo-microscope

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.73 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 7 residues within 4Å: Chain A: H.174 Chain C: H.174 Chain E: H.174 Chain K: H.174 Ligands: FE.5, FE.9, FE.21 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain K, 1 interactions with chain E Metal complexes: C:H.174, A:H.174, K:H.174, E:H.174 FE.3: 7 residues within 4Å: Chain B: H.174 Chain G: H.174 Chain I: H.174 Chain R: H.174 Ligands: FE.13, FE.17, FE.35 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain I, 1 interactions with chain B, 1 interactions with chain R Metal complexes: G:H.174, I:H.174, B:H.174, R:H.174 FE.5: 7 residues within 4Å: Chain A: H.174 Chain C: H.174 Chain E: H.174 Chain K: H.174 Ligands: FE.1, FE.9, FE.21 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain K, 1 interactions with chain E Metal complexes: C:H.174, A:H.174, K:H.174, E:H.174 FE.7: 7 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain M: H.174 Chain V: H.174 Ligands: FE.19, FE.25, FE.43 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain M, 1 interactions with chain V Metal complexes: J:H.174, D:H.174, M:H.174, V:H.174 FE.9: 7 residues within 4Å: Chain A: H.174 Chain C: H.174 Chain E: H.174 Chain K: H.174 Ligands: FE.1, FE.5, FE.21 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain K, 1 interactions with chain E Metal complexes: C:H.174, A:H.174, K:H.174, E:H.174 FE.11: 7 residues within 4Å: Chain F: H.174 Chain H: H.174 Chain P: H.174 Chain T: H.174 Ligands: FE.15, FE.31, FE.39 4 PLIP interactions: 1 interactions with chain H, 1 interactions with chain F, 1 interactions with chain T, 1 interactions with chain P Metal complexes: H:H.174, F:H.174, T:H.174, P:H.174 FE.13: 7 residues within 4Å: Chain B: H.174 Chain G: H.174 Chain I: H.174 Chain R: H.174 Ligands: FE.3, FE.17, FE.35 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain I, 1 interactions with chain B, 1 interactions with chain R Metal complexes: G:H.174, I:H.174, B:H.174, R:H.174 FE.15: 7 residues within 4Å: Chain F: H.174 Chain H: H.174 Chain P: H.174 Chain T: H.174 Ligands: FE.11, FE.31, FE.39 4 PLIP interactions: 1 interactions with chain H, 1 interactions with chain F, 1 interactions with chain T, 1 interactions with chain P Metal complexes: H:H.174, F:H.174, T:H.174, P:H.174 FE.17: 7 residues within 4Å: Chain B: H.174 Chain G: H.174 Chain I: H.174 Chain R: H.174 Ligands: FE.3, FE.13, FE.35 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain G, 1 interactions with chain R, 1 interactions with chain I Metal complexes: B:H.174, G:H.174, R:H.174, I:H.174 FE.19: 7 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain M: H.174 Chain V: H.174 Ligands: FE.7, FE.25, FE.43 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain V, 1 interactions with chain M Metal complexes: J:H.174, D:H.174, V:H.174, M:H.174 FE.21: 7 residues within 4Å: Chain A: H.174 Chain C: H.174 Chain E: H.174 Chain K: H.174 Ligands: FE.1, FE.5, FE.9 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain K Metal complexes: E:H.174, A:H.174, C:H.174, K:H.174 FE.23: 7 residues within 4Å: Chain L: H.174 Chain N: H.174 Chain O: H.174 Chain X: H.174 Ligands: FE.27, FE.29, FE.47 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain X, 1 interactions with chain O, 1 interactions with chain N Metal complexes: L:H.174, X:H.174, O:H.174, N:H.174 FE.25: 7 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain M: H.174 Chain V: H.174 Ligands: FE.7, FE.19, FE.43 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain V, 1 interactions with chain M Metal complexes: J:H.174, D:H.174, V:H.174, M:H.174 FE.27: 7 residues within 4Å: Chain L: H.174 Chain N: H.174 Chain O: H.174 Chain X: H.174 Ligands: FE.23, FE.29, FE.47 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain X, 1 interactions with chain O, 1 interactions with chain N Metal complexes: L:H.174, X:H.174, O:H.174, N:H.174 FE.29: 7 residues within 4Å: Chain L: H.174 Chain N: H.174 Chain O: H.174 Chain X: H.174 Ligands: FE.23, FE.27, FE.47 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain X, 1 interactions with chain O, 1 interactions with chain N Metal complexes: L:H.174, X:H.174, O:H.174, N:H.174 FE.31: 7 residues within 4Å: Chain F: H.174 Chain H: H.174 Chain P: H.174 Chain T: H.174 Ligands: FE.11, FE.15, FE.39 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain T, 1 interactions with chain H, 1 interactions with chain P Metal complexes: F:H.174, T:H.174, H:H.174, P:H.174 FE.33: 7 residues within 4Å: Chain Q: H.174 Chain S: H.174 Chain U: H.174 Chain W: H.174 Ligands: FE.37, FE.41, FE.45 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain Q, 1 interactions with chain S, 1 interactions with chain W Metal complexes: U:H.174, Q:H.174, S:H.174, W:H.174 FE.35: 7 residues within 4Å: Chain B: H.174 Chain G: H.174 Chain I: H.174 Chain R: H.174 Ligands: FE.3, FE.13, FE.17 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain I, 1 interactions with chain G, 1 interactions with chain R Metal complexes: B:H.174, I:H.174, G:H.174, R:H.174 FE.37: 7 residues within 4Å: Chain Q: H.174 Chain S: H.174 Chain U: H.174 Chain W: H.174 Ligands: FE.33, FE.41, FE.45 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain Q, 1 interactions with chain S, 1 interactions with chain W Metal complexes: U:H.174, Q:H.174, S:H.174, W:H.174 FE.39: 7 residues within 4Å: Chain F: H.174 Chain H: H.174 Chain P: H.174 Chain T: H.174 Ligands: FE.11, FE.15, FE.31 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain T, 1 interactions with chain H, 1 interactions with chain P Metal complexes: F:H.174, T:H.174, H:H.174, P:H.174 FE.41: 7 residues within 4Å: Chain Q: H.174 Chain S: H.174 Chain U: H.174 Chain W: H.174 Ligands: FE.33, FE.37, FE.45 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain Q, 1 interactions with chain S, 1 interactions with chain W Metal complexes: U:H.174, Q:H.174, S:H.174, W:H.174 FE.43: 7 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain M: H.174 Chain V: H.174 Ligands: FE.7, FE.19, FE.25 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain V, 1 interactions with chain D, 1 interactions with chain M Metal complexes: J:H.174, V:H.174, D:H.174, M:H.174 FE.45: 7 residues within 4Å: Chain Q: H.174 Chain S: H.174 Chain U: H.174 Chain W: H.174 Ligands: FE.33, FE.37, FE.41 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain Q, 1 interactions with chain S, 1 interactions with chain W Metal complexes: U:H.174, Q:H.174, S:H.174, W:H.174 FE.47: 7 residues within 4Å: Chain L: H.174 Chain N: H.174 Chain O: H.174 Chain X: H.174 Ligands: FE.23, FE.27, FE.29 4 PLIP interactions: 1 interactions with chain N, 1 interactions with chain X, 1 interactions with chain L, 1 interactions with chain O Metal complexes: N:H.174, X:H.174, L:H.174, O:H.174

24 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.66, H2O.1 MG.4: 4 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.66, H2O.4 MG.6: 4 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.66, H2O.6 MG.8: 4 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.66, H2O.9 MG.10: 4 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.66, H2O.12 MG.12: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.66, H2O.15 MG.14: 4 residues within 4Å: Chain G: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.66, H2O.17 MG.16: 4 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.66, H2O.20 MG.18: 4 residues within 4Å: Chain I: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.66, H2O.23 MG.20: 4 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.66, H2O.26 MG.22: 4 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:H.66, H2O.28 MG.24: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.66, H2O.31 MG.26: 4 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:H.66, H2O.34 MG.28: 4 residues within 4Å: Chain N: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.66, H2O.37 MG.30: 4 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:H.66, H2O.40 MG.32: 4 residues within 4Å: Chain P: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:H.66, H2O.42 MG.34: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:H.66, H2O.45 MG.36: 4 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:H.66, H2O.48 MG.38: 4 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:H.66, H2O.51 MG.40: 4 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:H.66, H2O.53 MG.42: 4 residues within 4Å: Chain U: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:H.66, H2O.56 MG.44: 4 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:H.66, H2O.59 MG.46: 4 residues within 4Å: Chain W: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:H.66, H2O.62 MG.48: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 2 PLIP interactions: 1 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:H.66, H2O.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamdi, F. et al., 2.7 angstrom cryo-EM structure of vitrified M. musculus H-chain apoferritin from a compact 200 keV cryo-microscope. Plos One (2020)

Release Date

2020-05-13

Peptides

Ferritin heavy chain: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

O
A

P
A

Q
A

R
A

S
A

T
A

U
A

V
A

W
A

X
A

Ferritin heavy chain

Related Entries With Identical Sequence