SMTL ID : 8pp3.1 (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.2 FE.3: 4 residues within 4Å: Chain B: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.28, B:E.63, B:H.66, H2O.5, H2O.5 FE.4: 5 residues within 4Å: Chain C: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.28, C:E.63, C:H.66, H2O.8, H2O.8 FE.6: 5 residues within 4Å: Chain D: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.28, D:E.63, D:H.66, H2O.12, H2O.13 FE.7: 4 residues within 4Å: Chain E: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.28, E:E.63, E:H.66, H2O.17, H2O.18 FE.10: 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.21, H2O.21 FE.11: 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.25, H2O.26 FE.13: 4 residues within 4Å: Chain H: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.28, H:E.63, H:H.66, H2O.29, H2O.29 FE.14: 5 residues within 4Å: Chain I: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.28, I:E.63, I:H.66, H2O.32, H2O.32 FE.16: 5 residues within 4Å: Chain J: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.28, J:E.63, J:H.66, H2O.36, H2O.37 FE.17: 4 residues within 4Å: Chain K: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.28, K:E.63, K:H.66, H2O.41, H2O.42 FE.20: 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.45, H2O.45 FE.21: 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.49, H2O.49 FE.23: 4 residues within 4Å: Chain N: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.28, N:E.63, N:H.66, H2O.52, H2O.53 FE.24: 5 residues within 4Å: Chain O: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.28, O:E.63, O:H.66, H2O.56, H2O.56 FE.26: 5 residues within 4Å: Chain P: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.28, P:E.63, P:H.66, H2O.60, H2O.61 FE.27: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.28, Q:E.63, Q:H.66, H2O.65, H2O.65 FE.30: 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.69, H2O.69 FE.31: 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.73, H2O.73 FE.33: 4 residues within 4Å: Chain T: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.28, T:E.63, T:H.66, H2O.76, H2O.77 FE.34: 5 residues within 4Å: Chain U: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.28, U:E.63, U:H.66, H2O.80, H2O.80 FE.36: 5 residues within 4Å: Chain V: E.28, E.63, H.66, V.111, Q.142 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.28, V:E.63, V:H.66, H2O.84, H2O.85 FE.37: 4 residues within 4Å: Chain W: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.28, W:E.63, W:H.66, H2O.89, H2O.89 FE.40: 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.92, H2O.93

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.68, K.72 Chain B: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain D: E.68, K.72 Chain E: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain F: Y.40, D.43, L.57 Chain U: E.68, K.72 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain F: E.68, K.72 Chain U: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain G: E.68, K.72 Chain H: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain J: E.68, K.72 Chain K: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain L: Y.40, D.43, L.57 Chain O: E.68, K.72 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain L: E.68, K.72 Chain O: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain M: E.68, K.72 Chain N: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain P: E.68, K.72 Chain Q: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: E.68, K.72 Chain R: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain C: Y.40, D.43, L.57 Chain R: E.68, K.72 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain S: E.68, K.72 Chain T: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain V: E.68, K.72 Chain W: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain I: E.68, K.72 Chain X: Y.40, D.43, L.57 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain I: Y.40, D.43, L.57 Chain X: E.68, K.72 Ligand excluded by 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
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

M
A

N
B

O
C

P
D

Q
E

R
F

S
A

T
B

U
C

V
D

W
E

X
F

Ferritin heavy chain

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