SMTL ID : 9jqd.1

Cryo-EM structure of ferritin variant R63MeH/R67MeH

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.28, A:E.63, A:H.66, H2O.3 FE.2: 4 residues within 4Å: Chain A: S.60, H.61 Chain V: H.64, H.68 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.60, A:H.61 FE.3: 4 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.28, B:E.63, B:H.66, H2O.8 FE.4: 4 residues within 4Å: Chain B: S.60, H.61 Chain X: H.64, H.68 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.60, B:H.61 FE.5: 4 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.28, C:E.63, C:H.66, H2O.13 FE.6: 4 residues within 4Å: Chain C: S.60, H.61 Chain L: H.64, H.68 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.60, C:H.61 FE.7: 4 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.28, D:E.63, D:H.66, H2O.18 FE.8: 4 residues within 4Å: Chain D: S.60, H.61 Chain N: H.64, H.68 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.60, D:H.61 FE.9: 4 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.28, E:E.63, E:H.66, H2O.23 FE.10: 4 residues within 4Å: Chain E: S.60, H.61 Chain P: H.64, H.68 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.60, E:H.61 FE.11: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.28, F:E.63, F:H.66, H2O.28 FE.12: 4 residues within 4Å: Chain F: S.60, H.61 Chain W: H.64, H.68 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.60, F:H.61 FE.13: 4 residues within 4Å: Chain G: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.28, G:E.63, G:H.66, H2O.33 FE.14: 4 residues within 4Å: Chain G: S.60, H.61 Chain T: H.64, H.68 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:S.60, G:H.61 FE.15: 4 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.28, H:E.63, H:H.66, H2O.37 FE.16: 4 residues within 4Å: Chain H: S.60, H.61 Chain Q: H.64, H.68 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:S.60, H:H.61 FE.17: 4 residues within 4Å: Chain I: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.28, I:E.63, I:H.66, H2O.42 FE.18: 4 residues within 4Å: Chain I: S.60, H.61 Chain R: H.64, H.68 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:S.60, I:H.61 FE.19: 4 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.28, J:E.63, J:H.66, H2O.47 FE.20: 4 residues within 4Å: Chain J: S.60, H.61 Chain M: H.64, H.68 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:S.60, J:H.61 FE.21: 4 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.28, K:E.63, K:H.66, H2O.52 FE.22: 4 residues within 4Å: Chain K: S.60, H.61 Chain U: H.64, H.68 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:S.60, K:H.61 FE.23: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.28, L:E.63, L:H.66, H2O.57 FE.24: 4 residues within 4Å: Chain C: H.64, H.68 Chain L: S.60, H.61 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:S.60, L:H.61 FE.25: 4 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.28, M:E.63, M:H.66, H2O.62 FE.26: 4 residues within 4Å: Chain J: H.64, H.68 Chain M: S.60, H.61 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:S.60, M:H.61 FE.27: 4 residues within 4Å: Chain N: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.28, N:E.63, N:H.66, H2O.67 FE.28: 4 residues within 4Å: Chain D: H.64, H.68 Chain N: S.60, H.61 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:S.60, N:H.61 FE.29: 4 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.28, O:E.63, O:H.66, H2O.72 FE.30: 4 residues within 4Å: Chain O: S.60, H.61 Chain S: H.64, H.68 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:S.60, O:H.61 FE.31: 4 residues within 4Å: Chain P: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.28, P:E.63, P:H.66, H2O.77 FE.32: 4 residues within 4Å: Chain E: H.64, H.68 Chain P: S.60, H.61 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:S.60, P:H.61 FE.33: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.28, Q:E.63, Q:H.66, H2O.82 FE.34: 4 residues within 4Å: Chain H: H.64, H.68 Chain Q: S.60, H.61 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:S.60, Q:H.61 FE.35: 4 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.28, R:E.63, R:H.66, H2O.87 FE.36: 4 residues within 4Å: Chain I: H.64, H.68 Chain R: S.60, H.61 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:S.60, R:H.61 FE.37: 4 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.28, S:E.63, S:H.66, H2O.92 FE.38: 4 residues within 4Å: Chain O: H.64, H.68 Chain S: S.60, H.61 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:S.60, S:H.61 FE.39: 4 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.28, T:E.63, T:H.66, H2O.97 FE.40: 4 residues within 4Å: Chain G: H.64, H.68 Chain T: S.60, H.61 2 PLIP interactions: 2 interactions with chain T Metal complexes: T:S.60, T:H.61 FE.41: 4 residues within 4Å: Chain U: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.28, U:E.63, U:H.66, H2O.102 FE.42: 4 residues within 4Å: Chain K: H.64, H.68 Chain U: S.60, H.61 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:S.60, U:H.61 FE.43: 4 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.28, V:E.63, V:H.66, H2O.107 FE.44: 4 residues within 4Å: Chain A: H.64, H.68 Chain V: S.60, H.61 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:S.60, V:H.61 FE.45: 4 residues within 4Å: Chain W: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.28, W:E.63, W:H.66, H2O.112 FE.46: 4 residues within 4Å: Chain F: H.64, H.68 Chain W: S.60, H.61 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:S.60, W:H.61 FE.47: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.28, X:E.63, X:H.66, H2O.117 FE.48: 4 residues within 4Å: Chain B: H.64, H.68 Chain X: S.60, H.61 2 PLIP interactions: 2 interactions with chain X Metal complexes: X:S.60, X:H.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsou, J.C. et al., Site-Specific Histidine Aza-Michael Addition in Proteins Enabled by a Ferritin-Based Metalloenzyme. J.Am.Chem.Soc. (2024)

Release Date

2024-11-27

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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