SMTL ID : 8cpm.1

Human apoferritin after 405 nm laser exposure

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

24 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.4: 4 residues within 4Å: Chain B: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain C: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain D: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.12: 4 residues within 4Å: Chain E: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.14: 4 residues within 4Å: Chain F: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.16: 4 residues within 4Å: Chain G: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.17: 4 residues within 4Å: Chain H: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.18: 4 residues within 4Å: Chain I: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.20: 4 residues within 4Å: Chain J: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.23: 4 residues within 4Å: Chain K: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain L: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.25: 4 residues within 4Å: Chain M: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.27: 4 residues within 4Å: Chain N: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.29: 4 residues within 4Å: Chain O: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.30: 4 residues within 4Å: Chain P: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.31: 4 residues within 4Å: Chain Q: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.32: 4 residues within 4Å: Chain R: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.33: 4 residues within 4Å: Chain S: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.34: 4 residues within 4Å: Chain T: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.35: 4 residues within 4Å: Chain U: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.36: 4 residues within 4Å: Chain V: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.37: 4 residues within 4Å: Chain W: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP NA.38: 4 residues within 4Å: Chain X: E.24, E.59, H.62, Q.138 Ligand excluded by PLIP

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.128, E.131 Chain G: D.128, E.131 Chain U: D.128, E.131 5 PLIP interactions: 1 interactions with chain U, 1 interactions with chain A, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: U:E.131, A:E.131, G:E.131, H2O.20, H2O.64 MG.3: 5 residues within 4Å: Chain A: H.170 Chain E: H.170 Chain F: H.170 Chain X: L.166, H.170 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain X, 1 interactions with chain F, 1 interactions with chain E Metal complexes: A:H.170, X:H.170, F:H.170, E:H.170 MG.5: 6 residues within 4Å: Chain B: H.170 Chain C: H.170 Chain S: L.166, H.170 Chain U: L.166, H.170 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain U, 1 interactions with chain C, 1 interactions with chain S Metal complexes: B:H.170, U:H.170, C:H.170, S:H.170 MG.6: 6 residues within 4Å: Chain B: D.128, E.131 Chain K: D.128, E.131 Chain R: D.128, E.131 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain K, 1 interactions with chain R, 2 Ligand-Water interactions Metal complexes: B:E.131, K:E.131, R:E.131, H2O.5, H2O.55 MG.8: 6 residues within 4Å: Chain C: D.128, E.131 Chain Q: D.128, E.131 Chain X: D.128, E.131 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain X, 1 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: C:E.131, X:E.131, Q:E.131, H2O.52, H2O.74 MG.10: 6 residues within 4Å: Chain D: H.170 Chain G: H.170 Chain H: L.166, H.170 Chain T: L.166, H.170 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain T, 1 interactions with chain D, 1 interactions with chain H Metal complexes: G:H.170, T:H.170, D:H.170, H:H.170 MG.11: 6 residues within 4Å: Chain D: D.128, E.131 Chain I: D.128, E.131 Chain S: D.128, E.131 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain S, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: D:E.131, S:E.131, I:E.131, H2O.11, H2O.58 MG.13: 6 residues within 4Å: Chain E: D.128, E.131 Chain H: D.128, E.131 Chain W: D.128, E.131 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E, 1 interactions with chain W, 2 Ligand-Water interactions Metal complexes: H:E.131, E:E.131, W:E.131, H2O.14, H2O.23 MG.15: 6 residues within 4Å: Chain F: D.128, E.131 Chain N: D.128, E.131 Chain O: D.128, E.131 5 PLIP interactions: 1 interactions with chain N, 1 interactions with chain F, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: N:E.131, F:E.131, O:E.131, H2O.17, H2O.42 MG.19: 6 residues within 4Å: Chain I: L.166, H.170 Chain K: L.166, H.170 Chain L: H.170 Chain M: H.170 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 1 interactions with chain M, 1 interactions with chain I Metal complexes: L:H.170, K:H.170, M:H.170, I:H.170 MG.21: 6 residues within 4Å: Chain J: D.128, E.131 Chain L: D.128, E.131 Chain T: D.128, E.131 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain L, 1 interactions with chain T, 2 Ligand-Water interactions Metal complexes: J:E.131, L:E.131, T:E.131, H2O.30, H2O.61 MG.22: 6 residues within 4Å: Chain J: H.170 Chain O: H.170 Chain V: L.166, H.170 Chain W: L.166, H.170 4 PLIP interactions: 1 interactions with chain W, 1 interactions with chain V, 1 interactions with chain J, 1 interactions with chain O Metal complexes: W:H.170, V:H.170, J:H.170, O:H.170 MG.26: 6 residues within 4Å: Chain M: D.128, E.131 Chain P: D.128, E.131 Chain V: D.128, E.131 5 PLIP interactions: 1 interactions with chain M, 1 interactions with chain V, 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: M:E.131, V:E.131, P:E.131, H2O.39, H2O.68 MG.28: 5 residues within 4Å: Chain N: L.166, H.170 Chain P: H.170 Chain Q: H.170 Chain R: H.170 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain Q, 1 interactions with chain N, 1 interactions with chain P Metal complexes: R:H.170, Q:H.170, N:H.170, P:H.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Last, M.G.F. et al., Super-resolution fluorescence imaging of cryosamples does not limit achievable resolution in cryoEM. J.Struct.Biol. (2023)

Release Date

2023-03-15

Peptides

Ferritin heavy chain, N-terminally processed: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
4

D
6

E
A

F
B

G
E

H
F

I
G

J
H

K
I

L
K

M
M

N
O

O
P

P
Q

Q
S

R
U

S
W

T
X

U
Y

V
a

W
e

X
r

Ferritin heavy chain, N-terminally processed

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