SMTL ID : 8tue.1

Cryo-EM structure of Apoferritin collected by Leginon on Glacios at 2.1 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: E.28, E.63, H.66, V.111, Y.138, E.141, Q.142 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.28, A:E.28, A:E.63, A:H.66 ZN.2: 4 residues within 4Å: Chain B: H.66, Y.137, Y.138, E.141 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.66, B:Y.137, B:E.141 ZN.4: 4 residues within 4Å: Chain C: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.66, C:H.66 ZN.6: 4 residues within 4Å: Chain D: H.66, Y.137, Y.138, E.141 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.66, D:H.66 ZN.7: 7 residues within 4Å: Chain E: E.28, E.63, H.66, V.111, Y.138, E.141, Q.142 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.28, E:E.28, E:E.63, E:H.66 ZN.8: 4 residues within 4Å: Chain F: H.66, Y.137, Y.138, E.141 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.66, F:H.66, F:Y.137, F:E.141 ZN.9: 4 residues within 4Å: Chain G: H.66, Y.137, Y.138, E.141 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.66, G:H.66 ZN.10: 4 residues within 4Å: Chain H: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.66, H:H.66 ZN.12: 4 residues within 4Å: Chain I: H.66, Y.137, Y.138, E.141 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.66, I:H.66 ZN.13: 4 residues within 4Å: Chain J: H.66, Y.137, Y.138, E.141 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:H.66, J:H.66 ZN.14: 4 residues within 4Å: Chain K: H.66, Y.137, Y.138, E.141 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:H.66, K:H.66 ZN.15: 4 residues within 4Å: Chain L: H.66, Y.137, Y.138, E.141 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:H.66, L:H.66 ZN.16: 4 residues within 4Å: Chain M: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:H.66, M:H.66 ZN.17: 4 residues within 4Å: Chain N: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:H.66, N:H.66 ZN.18: 7 residues within 4Å: Chain O: E.28, E.63, H.66, V.111, Y.138, E.141, Q.142 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.28, O:E.28, O:E.63, O:H.66 ZN.20: 7 residues within 4Å: Chain P: E.28, E.63, H.66, V.111, Y.138, E.141, Q.142 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:E.28, P:E.28, P:E.63, P:H.66 ZN.22: 4 residues within 4Å: Chain Q: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:H.66, Q:H.66 ZN.23: 4 residues within 4Å: Chain R: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:H.66, R:H.66 ZN.24: 4 residues within 4Å: Chain S: H.66, Y.137, Y.138, E.141 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:H.66, S:H.66 ZN.25: 4 residues within 4Å: Chain T: H.66, Y.137, Y.138, E.141 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:H.66, T:H.66, T:Y.137, T:E.141 ZN.26: 7 residues within 4Å: Chain U: E.28, E.63, H.66, V.111, Y.138, E.141, Q.142 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.28, U:E.28, U:E.63, U:H.66 ZN.27: 4 residues within 4Å: Chain V: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:H.66, V:H.66 ZN.29: 4 residues within 4Å: Chain W: E.28, H.66, Y.138, E.141 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:H.66, W:H.66 ZN.30: 7 residues within 4Å: Chain X: E.28, E.63, H.66, V.111, Y.138, E.141, Q.142 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:E.28, X:E.28, X:E.63, X:H.66

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

FE.3: 8 residues within 4Å: Chain C: L.170, H.174 Chain G: L.170, H.174 Chain K: L.170, H.174 Chain T: L.170, H.174 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C, 1 interactions with chain K, 1 interactions with chain T Metal complexes: G:H.174, C:H.174, K:H.174, T:H.174 FE.5: 8 residues within 4Å: Chain D: L.170, H.174 Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain D, 1 interactions with chain L, 1 interactions with chain F Metal complexes: R:H.174, D:H.174, L:H.174, F:H.174 FE.11: 8 residues within 4Å: Chain I: L.170, H.174 Chain J: L.170, H.174 Chain M: L.170, H.174 Chain N: L.170, H.174 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J, 1 interactions with chain N, 1 interactions with chain M Metal complexes: I:H.174, J:H.174, N:H.174, M:H.174 FE.19: 8 residues within 4Å: Chain B: L.170, H.174 Chain H: L.170, H.174 Chain O: L.170, H.174 Chain P: L.170, H.174 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H, 1 interactions with chain P, 1 interactions with chain O Metal complexes: B:H.174, H:H.174, P:H.174, O:H.174 FE.21: 8 residues within 4Å: Chain Q: L.170, H.174 Chain S: L.170, H.174 Chain U: L.170, H.174 Chain X: L.170, H.174 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain Q, 1 interactions with chain U, 1 interactions with chain S Metal complexes: X:H.174, Q:H.174, U:H.174, S:H.174 FE.28: 8 residues within 4Å: Chain A: L.170, H.174 Chain E: L.170, H.174 Chain V: L.170, H.174 Chain W: L.170, H.174 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain V, 1 interactions with chain W Metal complexes: E:H.174, A:H.174, V:H.174, W:H.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, L. et al., Cryo-EM structure of Apoferritin collected by Leginon on Glacios at 2.1 Angstrom resolution. To Be Published

Release Date

2024-09-04

Peptides

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
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

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