SMTL ID : 8pp4.1 (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: 4 residues within 4Å: Chain A: E.28, E.63, H.66, V.111 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: 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.6 FE.4: 4 residues within 4Å: Chain C: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.28, C:E.63, C:H.66, H2O.10, H2O.11 FE.5: 5 residues within 4Å: Chain C: Y.169, L.170, K.173, H.174 Chain U: H.174 No protein-ligand interaction detected (PLIP) FE.7: 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.13, H2O.13 FE.10: 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.11: 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.12: 4 residues within 4Å: Chain G: E.28, E.63, H.66, V.111 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.25 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.15: 4 residues within 4Å: Chain I: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.28, I:E.63, I:H.66, H2O.34, H2O.34 FE.16: 5 residues within 4Å: Chain I: Y.169, L.170, K.173, H.174 Chain O: H.174 No protein-ligand interaction detected (PLIP) FE.18: 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.37, H2O.37 FE.21: 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.22: 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.23: 4 residues within 4Å: Chain M: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.28, M:E.63, M:H.66, H2O.48, H2O.48 FE.24: 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.53, H2O.53 FE.26: 4 residues within 4Å: Chain O: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.28, O:E.63, O:H.66, H2O.58, H2O.58 FE.27: 5 residues within 4Å: Chain C: H.174 Chain O: Y.169, L.170, K.173, H.174 No protein-ligand interaction detected (PLIP) FE.29: 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.60, H2O.61 FE.32: 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.66 FE.33: 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.68, H2O.68 FE.34: 4 residues within 4Å: Chain S: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.28, S:E.63, S:H.66, H2O.72, H2O.72 FE.35: 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.37: 4 residues within 4Å: Chain U: E.28, E.63, H.66, V.111 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.28, U:E.63, U:H.66, H2O.81, H2O.82 FE.38: 5 residues within 4Å: Chain I: H.174 Chain U: Y.169, L.170, K.173, H.174 No protein-ligand interaction detected (PLIP) FE.40: 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.84, H2O.84 FE.43: 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.88, H2O.89 FE.44: 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.92

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: E.135 Chain C: E.135 Chain M: E.135 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain D: E.135 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain D: D.132, E.135 Chain E: E.135 Chain F: E.135 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: E:E.135, D:D.132, H2O.17, H2O.21, H2O.21 MG.14: 3 residues within 4Å: Chain H: E.135 Chain I: E.135 Chain S: E.135 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain J: E.135 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain J: D.132, E.135 Chain K: E.135 Chain L: E.135 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: J:D.132, K:E.135, H2O.41, H2O.44, H2O.45 MG.25: 3 residues within 4Å: Chain G: E.135 Chain N: E.135 Chain O: E.135 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain P: E.135 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain P: D.132, E.135 Chain Q: E.135 Chain R: E.135 5 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain P, 3 Ligand-Water interactions Metal complexes: Q:E.135, P:D.132, H2O.64, H2O.68, H2O.69 MG.36: 3 residues within 4Å: Chain A: E.135 Chain T: E.135 Chain U: E.135 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain V: E.135 No protein-ligand interaction detected (PLIP) MG.42: 4 residues within 4Å: Chain V: D.132, E.135 Chain W: E.135 Chain X: E.135 5 PLIP interactions: 1 interactions with chain V, 1 interactions with chain W, 3 Ligand-Water interactions Metal complexes: V:D.132, W:E.135, H2O.88, H2O.92, H2O.92

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

CL.6: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: CL.17, CL.28, CL.39 Ligand excluded by PLIP CL.17: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: CL.6, CL.28, CL.39 Ligand excluded by PLIP CL.28: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: CL.6, CL.17, CL.39 Ligand excluded by PLIP CL.39: 11 residues within 4Å: Chain C: L.170, H.174 Chain I: L.170, H.174 Chain O: L.170, H.174 Chain U: L.170, H.174 Ligands: CL.6, CL.17, CL.28 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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