SMTL ID : 8pp3.2 (1 other biounit)

Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and crystal contact tuned negatively supercharged ferritin variant Ftn(neg)-m1 (Mg formate condition)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.28, A:E.63, A:H.66, H2O.1, H2O.1 FE.2: 5 residues within 4Å: Chain B: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.28, B:E.63, B:H.66, H2O.3, H2O.3 FE.4: 5 residues within 4Å: Chain C: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.28, C:E.63, C:H.66 FE.5: 4 residues within 4Å: Chain D: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.28, D:E.63, D:H.66, H2O.8, H2O.8 FE.7: 5 residues within 4Å: Chain E: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.28, E:E.63, E:H.66, H2O.11, H2O.11 FE.8: 5 residues within 4Å: Chain F: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.28, F:E.63, F:H.66, H2O.12, H2O.12 FE.9: 5 residues within 4Å: Chain G: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.28, G:E.63, G:H.66, H2O.14, H2O.15 FE.10: 5 residues within 4Å: Chain H: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.28, H:E.63, H:H.66, H2O.16, H2O.17 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:H.66 FE.13: 4 residues within 4Å: Chain J: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.28, J:E.63, J:H.66, H2O.21, H2O.22 FE.15: 5 residues within 4Å: Chain K: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.28, K:E.63, K:H.66, H2O.24, H2O.24 FE.16: 5 residues within 4Å: Chain L: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.28, L:E.63, L:H.66, H2O.26, H2O.26 FE.17: 5 residues within 4Å: Chain M: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.28, M:E.63, M:H.66, H2O.28, H2O.28 FE.18: 5 residues within 4Å: Chain N: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.28, N:E.63, N:H.66, H2O.30, H2O.30 FE.20: 5 residues within 4Å: Chain O: E.28, E.63, H.66, V.111, Q.142 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.28, O:E.63, O:H.66 FE.21: 4 residues within 4Å: Chain P: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.28, P:E.63, P:H.66, H2O.35, H2O.35 FE.23: 5 residues within 4Å: Chain Q: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.28, Q:E.63, Q:H.66, H2O.38, H2O.38 FE.24: 5 residues within 4Å: Chain R: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.28, R:E.63, R:H.66, H2O.39, H2O.39 FE.25: 5 residues within 4Å: Chain S: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.28, S:E.63, S:H.66, H2O.42, H2O.42 FE.26: 5 residues within 4Å: Chain T: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.28, T:E.63, T:H.66, H2O.44, H2O.44 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:H.66 FE.29: 4 residues within 4Å: Chain V: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.28, V:E.63, V:H.66, H2O.49, H2O.49 FE.31: 5 residues within 4Å: Chain W: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.28, W:E.63, W:H.66, H2O.51, H2O.52 FE.32: 5 residues within 4Å: Chain X: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.28, X:E.63, X:H.66, H2O.53, H2O.53

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: E.135 Chain F: E.135 Chain O: E.135 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain D: E.135 Chain E: E.135 Chain S: E.135 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain H: E.135 Chain L: E.135 Chain U: E.135 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain J: E.135 Chain K: E.135 Chain M: E.135 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain I: E.135 Chain N: E.135 Chain R: E.135 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: E.135 Chain P: E.135 Chain Q: E.135 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain C: E.135 Chain T: E.135 Chain X: E.135 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain G: E.135 Chain V: E.135 Chain W: E.135 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, L. et al., Assembly Requirements for the Construction of Large-Scale Binary Protein Structures. Biomacromolecules (2024)

Release Date

2023-12-27

Peptides

Ferritin heavy chain: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

G
G

H
H

I
I

J
J

K
K

L
L

M
G

N
H

O
I

P
J

Q
K

R
L

S
G

T
H

U
I

V
J

W
K

X
L

Ferritin heavy chain