SMTL ID : 8pp4.2 (1 other biounit)

Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and reduced charge negatively supercharged ferritin variant Ftn(neg)-m3 (Mg formate condition)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, A:E.62, A:H.65, H2O.1, H2O.2 FE.3: 5 residues within 4Å: Chain B: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.27, B:E.62, B:H.65, H2O.3, H2O.4 FE.6: 4 residues within 4Å: Chain C: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.27, C:E.62, C:H.65, H2O.5, H2O.6 FE.8: 4 residues within 4Å: Chain D: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.27, D:E.62, D:H.65, H2O.7, H2O.7 FE.10: 5 residues within 4Å: Chain E: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.27, E:E.62, E:H.65, H2O.9, H2O.9 FE.11: 5 residues within 4Å: Chain F: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.27, F:E.62, F:H.65, H2O.10, H2O.10 FE.12: 11 residues within 4Å: Chain F: H.173 Chain L: H.173 Chain R: H.173 Chain X: H.173 Ligands: CL.13, FE.25, CL.26, FE.38, CL.39, FE.51, CL.52 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain R Metal complexes: X:H.173, L:H.173, F:H.173, R:H.173 FE.14: 5 residues within 4Å: Chain G: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.27, G:E.62, G:H.65, H2O.12, H2O.12 FE.16: 5 residues within 4Å: Chain H: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.27, H:E.62, H:H.65, H2O.14, H2O.15 FE.19: 4 residues within 4Å: Chain I: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.27, I:E.62, I:H.65, H2O.15, H2O.17 FE.21: 4 residues within 4Å: Chain J: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.27, J:E.62, J:H.65, H2O.17, H2O.18 FE.23: 5 residues within 4Å: Chain K: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.27, K:E.62, K:H.65, H2O.19, H2O.19 FE.24: 5 residues within 4Å: Chain L: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.27, L:E.62, L:H.65, H2O.21, H2O.21 FE.25: 11 residues within 4Å: Chain F: H.173 Chain L: H.173 Chain R: H.173 Chain X: H.173 Ligands: FE.12, CL.13, CL.26, FE.38, CL.39, FE.51, CL.52 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain F, 1 interactions with chain X, 1 interactions with chain L Metal complexes: R:H.173, F:H.173, X:H.173, L:H.173 FE.27: 5 residues within 4Å: Chain M: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.27, M:E.62, M:H.65, H2O.23, H2O.23 FE.29: 5 residues within 4Å: Chain N: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.27, N:E.62, N:H.65, H2O.25, H2O.25 FE.32: 4 residues within 4Å: Chain O: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.27, O:E.62, O:H.65, H2O.26, H2O.27 FE.34: 4 residues within 4Å: Chain P: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.27, P:E.62, P:H.65, H2O.28, H2O.29 FE.36: 5 residues within 4Å: Chain Q: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.27, Q:E.62, Q:H.65, H2O.30, H2O.30 FE.37: 5 residues within 4Å: Chain R: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.27, R:E.62, R:H.65, H2O.32, H2O.32 FE.38: 11 residues within 4Å: Chain F: H.173 Chain L: H.173 Chain R: H.173 Chain X: H.173 Ligands: FE.12, CL.13, FE.25, CL.26, CL.39, FE.51, CL.52 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain R, 1 interactions with chain F, 1 interactions with chain L Metal complexes: X:H.173, R:H.173, F:H.173, L:H.173 FE.40: 5 residues within 4Å: Chain S: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.27, S:E.62, S:H.65, H2O.33, H2O.34 FE.42: 5 residues within 4Å: Chain T: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.27, T:E.62, T:H.65, H2O.35, H2O.36 FE.45: 4 residues within 4Å: Chain U: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.27, U:E.62, U:H.65, H2O.37, H2O.38 FE.47: 4 residues within 4Å: Chain V: E.27, E.62, H.65, V.110 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.27, V:E.62, V:H.65, H2O.39, H2O.39 FE.49: 5 residues within 4Å: Chain W: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.27, W:E.62, W:H.65, H2O.41, H2O.41 FE.50: 5 residues within 4Å: Chain X: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.27, X:E.62, X:H.65, H2O.42, H2O.43 FE.51: 11 residues within 4Å: Chain F: H.173 Chain L: H.173 Chain R: H.173 Chain X: H.173 Ligands: FE.12, CL.13, FE.25, CL.26, FE.38, CL.39, CL.52 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain X, 1 interactions with chain R Metal complexes: L:H.173, F:H.173, X:H.173, R:H.173

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 8 residues within 4Å: Chain A: L.169, H.173 Chain B: L.169, H.173 Chain C: L.169, H.173 Chain E: L.169, H.173 Ligand excluded by PLIP CL.13: 15 residues within 4Å: Chain F: L.169, H.173 Chain L: L.169, H.173 Chain R: L.169, H.173 Chain X: L.169, H.173 Ligands: FE.12, FE.25, CL.26, FE.38, CL.39, FE.51, CL.52 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain G: L.169, H.173 Chain H: L.169, H.173 Chain I: L.169, H.173 Chain K: L.169, H.173 Ligand excluded by PLIP CL.26: 15 residues within 4Å: Chain F: L.169, H.173 Chain L: L.169, H.173 Chain R: L.169, H.173 Chain X: L.169, H.173 Ligands: FE.12, CL.13, FE.25, FE.38, CL.39, FE.51, CL.52 Ligand excluded by PLIP CL.28: 8 residues within 4Å: Chain M: L.169, H.173 Chain N: L.169, H.173 Chain O: L.169, H.173 Chain Q: L.169, H.173 Ligand excluded by PLIP CL.39: 15 residues within 4Å: Chain F: L.169, H.173 Chain L: L.169, H.173 Chain R: L.169, H.173 Chain X: L.169, H.173 Ligands: FE.12, CL.13, FE.25, CL.26, FE.38, FE.51, CL.52 Ligand excluded by PLIP CL.41: 8 residues within 4Å: Chain S: L.169, H.173 Chain T: L.169, H.173 Chain U: L.169, H.173 Chain W: L.169, H.173 Ligand excluded by PLIP CL.52: 15 residues within 4Å: Chain F: L.169, H.173 Chain L: L.169, H.173 Chain R: L.169, H.173 Chain X: L.169, H.173 Ligands: FE.12, CL.13, FE.25, CL.26, FE.38, CL.39, FE.51 Ligand excluded by PLIP

16 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: E.134 Chain F: E.134 Chain Q: E.134 No protein-ligand interaction detected (PLIP) MG.5: 6 residues within 4Å: Chain B: D.131, E.134 Chain F: D.131, E.134 Chain Q: D.131, E.134 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.134 MG.7: 3 residues within 4Å: Chain C: E.134 Chain D: E.134 Chain S: E.134 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain C: D.131, E.134 Chain D: D.131, E.134 Chain S: D.131, E.134 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.131 MG.17: 3 residues within 4Å: Chain H: E.134 Chain L: E.134 Chain W: E.134 No protein-ligand interaction detected (PLIP) MG.18: 6 residues within 4Å: Chain H: D.131, E.134 Chain L: D.131, E.134 Chain W: D.131, E.134 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.134 MG.20: 3 residues within 4Å: Chain I: E.134 Chain J: E.134 Chain M: E.134 No protein-ligand interaction detected (PLIP) MG.22: 6 residues within 4Å: Chain I: D.131, E.134 Chain J: D.131, E.134 Chain M: D.131, E.134 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.131 MG.30: 3 residues within 4Å: Chain K: E.134 Chain N: E.134 Chain R: E.134 No protein-ligand interaction detected (PLIP) MG.31: 6 residues within 4Å: Chain K: D.131, E.134 Chain N: D.131, E.134 Chain R: D.131, E.134 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.134 MG.33: 3 residues within 4Å: Chain A: E.134 Chain O: E.134 Chain P: E.134 No protein-ligand interaction detected (PLIP) MG.35: 6 residues within 4Å: Chain A: D.131, E.134 Chain O: D.131, E.134 Chain P: D.131, E.134 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.131 MG.43: 3 residues within 4Å: Chain E: E.134 Chain T: E.134 Chain X: E.134 No protein-ligand interaction detected (PLIP) MG.44: 6 residues within 4Å: Chain E: D.131, E.134 Chain T: D.131, E.134 Chain X: D.131, E.134 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:E.134 MG.46: 3 residues within 4Å: Chain G: E.134 Chain U: E.134 Chain V: E.134 No protein-ligand interaction detected (PLIP) MG.48: 6 residues within 4Å: Chain G: D.131, E.134 Chain U: D.131, E.134 Chain V: D.131, E.134 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:D.131

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, N-terminally processed: 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, N-terminally processed