SMTL ID : 8rqb.1

Cryo-EM structure of mouse heavy-chain apoferritin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: H.169 Chain E: H.169 Chain F: H.169 Chain G: H.169 No protein-ligand interaction detected (PLIP) FE.3: 4 residues within 4Å: Chain B: H.169 Chain H: H.169 Chain L: H.169 Chain N: H.169 No protein-ligand interaction detected (PLIP) FE.5: 4 residues within 4Å: Chain C: H.169 Chain R: H.169 Chain S: H.169 Chain T: H.169 No protein-ligand interaction detected (PLIP) FE.8: 4 residues within 4Å: Chain D: H.169 Chain K: H.169 Chain M: H.169 Chain Q: H.169 No protein-ligand interaction detected (PLIP) FE.13: 4 residues within 4Å: Chain I: H.169 Chain J: H.169 Chain U: H.169 Chain V: H.169 No protein-ligand interaction detected (PLIP) FE.20: 4 residues within 4Å: Chain O: H.169 Chain P: H.169 Chain W: H.169 Chain X: H.169 No protein-ligand interaction detected (PLIP)

24 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.23, A:E.58, A:H.61, H2O.1, H2O.2 ZN.4: 4 residues within 4Å: Chain B: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.23, B:E.58, B:H.61, H2O.6, H2O.6 ZN.6: 4 residues within 4Å: Chain C: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.23, C:E.58, C:H.61, H2O.10, H2O.10 ZN.7: 4 residues within 4Å: Chain D: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.23, D:E.58, D:H.61, H2O.14, H2O.15 ZN.9: 4 residues within 4Å: Chain E: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.23, E:E.58, E:H.61, H2O.18, H2O.19 ZN.10: 4 residues within 4Å: Chain F: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.23, F:E.58, F:H.61, H2O.23, H2O.23 ZN.11: 4 residues within 4Å: Chain G: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.23, G:E.58, G:H.61, H2O.27, H2O.27 ZN.12: 4 residues within 4Å: Chain H: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.23, H:E.58, H:H.61, H2O.31, H2O.31 ZN.14: 4 residues within 4Å: Chain I: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.23, I:E.58, I:H.61, H2O.35, H2O.36 ZN.15: 4 residues within 4Å: Chain J: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.23, J:E.58, J:H.61, H2O.39, H2O.40 ZN.16: 4 residues within 4Å: Chain K: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.23, K:E.58, K:H.61, H2O.44, H2O.44 ZN.17: 4 residues within 4Å: Chain L: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.23, L:E.58, L:H.61, H2O.48, H2O.48 ZN.18: 4 residues within 4Å: Chain M: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.23, M:E.58, M:H.61, H2O.52, H2O.52 ZN.19: 4 residues within 4Å: Chain N: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.23, N:E.58, N:H.61, H2O.56, H2O.57 ZN.21: 4 residues within 4Å: Chain O: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.23, O:E.58, O:H.61, H2O.60, H2O.61 ZN.22: 4 residues within 4Å: Chain P: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.23, P:E.58, P:H.61, H2O.64, H2O.65 ZN.23: 4 residues within 4Å: Chain Q: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.23, Q:E.58, Q:H.61, H2O.69, H2O.69 ZN.24: 4 residues within 4Å: Chain R: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.23, R:E.58, R:H.61, H2O.73, H2O.73 ZN.25: 4 residues within 4Å: Chain S: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.23, S:E.58, S:H.61, H2O.77, H2O.77 ZN.26: 4 residues within 4Å: Chain T: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.23, T:E.58, T:H.61, H2O.81, H2O.82 ZN.27: 4 residues within 4Å: Chain U: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.23, U:E.58, U:H.61, H2O.85, H2O.86 ZN.28: 4 residues within 4Å: Chain V: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.23, V:E.58, V:H.61, H2O.90, H2O.90 ZN.29: 4 residues within 4Å: Chain W: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.23, W:E.58, W:H.61, H2O.94, H2O.94 ZN.30: 4 residues within 4Å: Chain X: E.23, E.58, H.61, Q.137 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.23, X:E.58, X:H.61, H2O.98, H2O.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kucukoglu, B. et al., Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution. Nat Commun (2024)

Release Date

2024-03-13

Peptides

Ferritin heavy chain, N-terminally processed: 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
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Ferritin heavy chain, N-terminally processed

Related Entries With Identical Sequence