SMTL ID : 5oba.1

Structure of a modified mouse H-chain ferritin with a lanthanide binding motif

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 3 residues within 4Å: Chain A: E.135 Chain B: E.135 Chain C: E.135 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:E.135, C:E.135, A:E.135 FE.2: 4 residues within 4Å: Chain A: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.28, A:E.63, A:E.63 FE.3: 4 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.28, B:E.63, B:E.63 FE.4: 4 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.28, C:E.63, C:E.63 FE.5: 4 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.28, D:E.63 FE.6: 3 residues within 4Å: Chain D: E.135 Chain E: E.135 Chain F: E.135 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.135 FE.7: 4 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.28, E:E.63, E:E.63 FE.8: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.28, F:E.63 FE.9: 3 residues within 4Å: Chain G: E.135 Chain H: E.135 Chain I: E.135 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: G:E.135, H:E.135, I:E.135, H2O.1 FE.10: 5 residues within 4Å: Chain G: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.28, G:E.28, G:E.63 FE.11: 4 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.28, H:E.63, H:E.63, H:H.66 FE.12: 5 residues within 4Å: Chain I: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.28, I:E.63, I:E.63 FE.13: 4 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.28, J:E.63, J:E.63, J:H.66, H2O.1 FE.14: 4 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.28, K:E.63, K:H.66 FE.15: 3 residues within 4Å: Chain J: E.135 Chain K: E.135 Chain L: E.135 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 1 interactions with chain J Metal complexes: K:E.135, L:E.135, J:E.135 FE.16: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.28, L:E.28, L:E.63, L:E.63 FE.17: 5 residues within 4Å: Chain M: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.28, M:E.63, M:E.63 FE.18: 3 residues within 4Å: Chain M: E.135 Chain N: E.135 Chain O: E.135 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain N, 2 interactions with chain O Metal complexes: M:E.135, N:E.135, O:E.135, O:E.135 FE.19: 5 residues within 4Å: Chain N: E.28, E.63, H.66, V.111, Q.142 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.28, N:E.28, N:E.63, N:E.63 FE.20: 4 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.28, O:E.63, O:E.63 FE.21: 5 residues within 4Å: Chain P: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.28, P:E.63, P:H.66 FE.22: 3 residues within 4Å: Chain P: E.135 Chain Q: E.135 Chain R: E.135 3 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain P, 1 interactions with chain R Metal complexes: Q:E.135, P:E.135, R:E.135 FE.23: 5 residues within 4Å: Chain Q: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.28, Q:E.63, Q:E.63 FE.24: 5 residues within 4Å: Chain R: E.28, E.63, H.66, V.111, Q.142 2 PLIP interactions: 2 interactions with chain R Metal complexes: R:E.28, R:E.63 FE.25: 4 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.28, S:E.63, S:E.63 FE.26: 3 residues within 4Å: Chain S: E.135 Chain T: E.135 Chain U: E.135 4 PLIP interactions: 2 interactions with chain U, 1 interactions with chain T, 1 interactions with chain S Metal complexes: U:E.135, U:E.135, T:E.135, S:E.135 FE.27: 4 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.28, T:E.63, T:E.63 FE.28: 5 residues within 4Å: Chain U: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.28, U:E.63, U:E.63 FE.29: 4 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.28, V:E.28, V:E.63 FE.30: 6 residues within 4Å: Chain V: D.132, E.135 Chain W: D.132, E.135 Chain X: D.132, E.135 3 PLIP interactions: 1 interactions with chain V, 1 interactions with chain W, 1 interactions with chain X Metal complexes: V:E.135, W:E.135, X:E.135 FE.31: 5 residues within 4Å: Chain W: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.28, W:E.63, W:E.63 FE.32: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.28, X:E.63, X:H.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calisti, L. et al., Engineered ferritin for lanthanide binding. PLoS ONE (2018)

Release Date

2018-07-25

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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