SMTL ID : 5jkl.1 (1 other biounit)

Binary crystal structure of positively and negatively supercharged variants Ftn(pos) and Ftn(neg) from human heavy chain ferritin (Mg formate condition)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.28, E.63, H.66, 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: 11 residues within 4Å: Chain A: H.174 Chain G: H.174 Chain M: H.174 Chain S: H.174 Ligands: CL.5, FE.25, CL.28, FE.48, CL.51, FE.71, CL.74 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain M, 1 interactions with chain S, 1 interactions with chain A Metal complexes: G:H.174, M:H.174, S:H.174, A:H.174 FE.6: 4 residues within 4Å: Chain B: E.28, E.63, H.66, 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.5, H2O.7 FE.9: 3 residues within 4Å: Chain C: E.28, E.63, H.66 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.12: 4 residues within 4Å: Chain D: E.28, E.63, H.66, 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.15, H2O.15 FE.13: 5 residues within 4Å: Chain D: H.174 Chain N: H.174 Chain O: H.174 Chain Q: H.174 Ligands: CL.16 4 PLIP interactions: 1 interactions with chain N, 1 interactions with chain O, 1 interactions with chain D, 1 interactions with chain Q Metal complexes: N:H.174, O:H.174, D:H.174, Q:H.174 FE.17: 4 residues within 4Å: Chain E: E.28, E.63, H.66, 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.20, H2O.20 FE.20: 4 residues within 4Å: Chain F: E.28, E.63, H.66, 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.24, H2O.24 FE.21: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: CL.23, FE.44, CL.46, FE.67, CL.69, FE.90, CL.92 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.174, R:H.174, F:H.174, L:H.174 FE.24: 4 residues within 4Å: Chain G: E.28, E.63, H.66, 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.29, H2O.29 FE.25: 11 residues within 4Å: Chain A: H.174 Chain G: H.174 Chain M: H.174 Chain S: H.174 Ligands: FE.2, CL.5, CL.28, FE.48, CL.51, FE.71, CL.74 4 PLIP interactions: 1 interactions with chain S, 1 interactions with chain G, 1 interactions with chain A, 1 interactions with chain M Metal complexes: S:H.174, G:H.174, A:H.174, M:H.174 FE.29: 4 residues within 4Å: Chain H: E.28, E.63, H.66, 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.33, H2O.35 FE.32: 3 residues within 4Å: Chain I: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.28, I:E.63, I:H.66, H2O.38, H2O.39 FE.35: 4 residues within 4Å: Chain J: E.28, E.63, H.66, 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.43, H2O.43 FE.36: 5 residues within 4Å: Chain J: H.174 Chain T: H.174 Chain U: H.174 Chain W: H.174 Ligands: CL.39 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain T, 1 interactions with chain J Metal complexes: U:H.174, W:H.174, T:H.174, J:H.174 FE.40: 4 residues within 4Å: Chain K: E.28, E.63, H.66, 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.48, H2O.48 FE.43: 4 residues within 4Å: Chain L: E.28, E.63, H.66, 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.52, H2O.52 FE.44: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.21, CL.23, CL.46, FE.67, CL.69, FE.90, CL.92 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain R, 1 interactions with chain L, 1 interactions with chain F Metal complexes: X:H.174, R:H.174, L:H.174, F:H.174 FE.47: 4 residues within 4Å: Chain M: E.28, E.63, H.66, 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.57, H2O.57 FE.48: 11 residues within 4Å: Chain A: H.174 Chain G: H.174 Chain M: H.174 Chain S: H.174 Ligands: FE.2, CL.5, FE.25, CL.28, CL.51, FE.71, CL.74 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain S, 1 interactions with chain A, 1 interactions with chain M Metal complexes: G:H.174, S:H.174, A:H.174, M:H.174 FE.52: 4 residues within 4Å: Chain N: E.28, E.63, H.66, 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.61, H2O.63 FE.55: 3 residues within 4Å: Chain O: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.28, O:E.63, O:H.66, H2O.66, H2O.67 FE.58: 4 residues within 4Å: Chain P: E.28, E.63, H.66, 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.71, H2O.71 FE.59: 5 residues within 4Å: Chain H: H.174 Chain I: H.174 Chain K: H.174 Chain P: H.174 Ligands: CL.62 4 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I, 1 interactions with chain K, 1 interactions with chain P Metal complexes: H:H.174, I:H.174, K:H.174, P:H.174 FE.63: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, 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.76, H2O.76 FE.66: 4 residues within 4Å: Chain R: E.28, E.63, H.66, 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.80, H2O.80 FE.67: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.21, CL.23, FE.44, CL.46, CL.69, FE.90, CL.92 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain F, 1 interactions with chain R, 1 interactions with chain L Metal complexes: X:H.174, F:H.174, R:H.174, L:H.174 FE.70: 4 residues within 4Å: Chain S: E.28, E.63, H.66, 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.85, H2O.85 FE.71: 11 residues within 4Å: Chain A: H.174 Chain G: H.174 Chain M: H.174 Chain S: H.174 Ligands: FE.2, CL.5, FE.25, CL.28, FE.48, CL.51, CL.74 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A, 1 interactions with chain M, 1 interactions with chain S Metal complexes: G:H.174, A:H.174, M:H.174, S:H.174 FE.75: 4 residues within 4Å: Chain T: E.28, E.63, H.66, 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.89, H2O.91 FE.78: 3 residues within 4Å: Chain U: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.28, U:E.63, U:H.66, H2O.94, H2O.95 FE.81: 4 residues within 4Å: Chain V: E.28, E.63, H.66, 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.99, H2O.99 FE.82: 5 residues within 4Å: Chain B: H.174 Chain C: H.174 Chain E: H.174 Chain V: H.174 Ligands: CL.85 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 1 interactions with chain V, 1 interactions with chain B Metal complexes: E:H.174, C:H.174, V:H.174, B:H.174 FE.86: 4 residues within 4Å: Chain W: E.28, E.63, H.66, 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.104, H2O.104 FE.89: 4 residues within 4Å: Chain X: E.28, E.63, H.66, 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.108, H2O.108 FE.90: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.21, CL.23, FE.44, CL.46, FE.67, CL.69, CL.92 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain L, 1 interactions with chain X, 1 interactions with chain F Metal complexes: R:H.174, L:H.174, X:H.174, F:H.174

32 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.135 Chain C: E.135 Chain N: E.135 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: Q.59 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: Q.59 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain C: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain D: E.135 Chain E: E.135 Chain F: E.135 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: Q.59, E.62 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.62, H2O.16, H2O.18 MG.18: 3 residues within 4Å: Chain D: D.132 Chain E: D.132 Chain F: D.132 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain F: Q.59 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain G: E.135 Chain I: E.135 Chain T: E.135 No protein-ligand interaction detected (PLIP) MG.27: 1 residues within 4Å: Chain G: Q.59 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain H: Q.59 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain I: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.37: 3 residues within 4Å: Chain J: E.135 Chain K: E.135 Chain L: E.135 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain J: Q.59, E.62 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.62, H2O.44, H2O.46 MG.41: 3 residues within 4Å: Chain J: D.132 Chain K: D.132 Chain L: D.132 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Chain L: Q.59 No protein-ligand interaction detected (PLIP) MG.49: 3 residues within 4Å: Chain H: E.135 Chain M: E.135 Chain O: E.135 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain M: Q.59 No protein-ligand interaction detected (PLIP) MG.53: 1 residues within 4Å: Chain N: Q.59 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain O: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.60: 3 residues within 4Å: Chain P: E.135 Chain Q: E.135 Chain R: E.135 No protein-ligand interaction detected (PLIP) MG.61: 2 residues within 4Å: Chain P: Q.59, E.62 3 PLIP interactions: 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.62, H2O.72, H2O.74 MG.64: 3 residues within 4Å: Chain P: D.132 Chain Q: D.132 Chain R: D.132 No protein-ligand interaction detected (PLIP) MG.68: 1 residues within 4Å: Chain R: Q.59 No protein-ligand interaction detected (PLIP) MG.72: 3 residues within 4Å: Chain B: E.135 Chain S: E.135 Chain U: E.135 No protein-ligand interaction detected (PLIP) MG.73: 1 residues within 4Å: Chain S: Q.59 No protein-ligand interaction detected (PLIP) MG.76: 1 residues within 4Å: Chain T: Q.59 No protein-ligand interaction detected (PLIP) MG.79: 3 residues within 4Å: Chain U: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.83: 3 residues within 4Å: Chain V: E.135 Chain W: E.135 Chain X: E.135 No protein-ligand interaction detected (PLIP) MG.84: 2 residues within 4Å: Chain V: Q.59, E.62 3 PLIP interactions: 1 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.62, H2O.100, H2O.102 MG.87: 3 residues within 4Å: Chain V: D.132 Chain W: D.132 Chain X: D.132 No protein-ligand interaction detected (PLIP) MG.91: 1 residues within 4Å: Chain X: Q.59 No protein-ligand interaction detected (PLIP)

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

CL.5: 13 residues within 4Å: Chain A: L.170, H.174 Chain G: H.174 Chain M: L.170, H.174 Chain S: H.174 Ligands: FE.2, FE.25, CL.28, FE.48, CL.51, FE.71, CL.74 Ligand excluded by PLIP CL.16: 7 residues within 4Å: Chain D: H.174 Chain N: L.170, H.174 Chain O: L.170, H.174 Chain Q: H.174 Ligands: FE.13 Ligand excluded by PLIP CL.23: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: FE.21, FE.44, CL.46, FE.67, CL.69, FE.90, CL.92 Ligand excluded by PLIP CL.28: 13 residues within 4Å: Chain A: H.174 Chain G: L.170, H.174 Chain M: H.174 Chain S: L.170, H.174 Ligands: FE.2, CL.5, FE.25, FE.48, CL.51, FE.71, CL.74 Ligand excluded by PLIP CL.39: 7 residues within 4Å: Chain J: H.174 Chain T: L.170, H.174 Chain U: L.170, H.174 Chain W: H.174 Ligands: FE.36 Ligand excluded by PLIP CL.46: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: FE.21, CL.23, FE.44, FE.67, CL.69, FE.90, CL.92 Ligand excluded by PLIP CL.51: 13 residues within 4Å: Chain A: H.174 Chain G: L.170, H.174 Chain M: L.170, H.174 Chain S: H.174 Ligands: FE.2, CL.5, FE.25, CL.28, FE.48, FE.71, CL.74 Ligand excluded by PLIP CL.62: 7 residues within 4Å: Chain H: L.170, H.174 Chain I: L.170, H.174 Chain K: H.174 Chain P: H.174 Ligands: FE.59 Ligand excluded by PLIP CL.69: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: FE.21, CL.23, FE.44, CL.46, FE.67, FE.90, CL.92 Ligand excluded by PLIP CL.74: 13 residues within 4Å: Chain A: L.170, H.174 Chain G: H.174 Chain M: H.174 Chain S: L.170, H.174 Ligands: FE.2, CL.5, FE.25, CL.28, FE.48, CL.51, FE.71 Ligand excluded by PLIP CL.85: 7 residues within 4Å: Chain B: L.170, H.174 Chain C: L.170, H.174 Chain E: H.174 Chain V: H.174 Ligands: FE.82 Ligand excluded by PLIP CL.92: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: FE.21, CL.23, FE.44, CL.46, FE.67, CL.69, FE.90 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: K.72 Chain B: Y.40, D.43 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.40, B:Y.40, B:D.43, A:K.72 GOL.11: 9 residues within 4Å: Chain A: D.132, E.135, T.136 Chain C: D.132, E.135, T.136 Chain N: D.132, E.135, T.136 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain N Hydrogen bonds: A:E.135, A:T.136, N:T.136 Water bridges: C:T.136 GOL.19: 3 residues within 4Å: Chain E: D.85 Chain X: Q.87, K.88 2 PLIP interactions: 1 interactions with chain X, 1 interactions with chain E Hydrogen bonds: X:K.88, E:D.85 GOL.31: 3 residues within 4Å: Chain G: K.72 Chain H: Y.40, D.43 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:Y.40, H:Y.40, H:D.43, G:K.72 GOL.34: 9 residues within 4Å: Chain G: D.132, E.135, T.136 Chain I: D.132, E.135, T.136 Chain T: D.132, E.135, T.136 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain T, 2 interactions with chain G Water bridges: I:T.136 Hydrogen bonds: T:T.136, G:E.135, G:T.136 GOL.42: 3 residues within 4Å: Chain K: D.85 Chain R: Q.87, K.88 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain K Hydrogen bonds: R:K.88, K:D.85 GOL.54: 3 residues within 4Å: Chain M: K.72 Chain N: Y.40, D.43 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:Y.40, N:Y.40, N:D.43, M:K.72 GOL.57: 9 residues within 4Å: Chain H: D.132, E.135, T.136 Chain M: D.132, E.135, T.136 Chain O: D.132, E.135, T.136 4 PLIP interactions: 2 interactions with chain M, 1 interactions with chain H, 1 interactions with chain O Hydrogen bonds: M:E.135, M:T.136, H:T.136 Water bridges: O:T.136 GOL.65: 3 residues within 4Å: Chain F: Q.87, K.88 Chain Q: D.85 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain Q Hydrogen bonds: F:K.88, Q:D.85 GOL.77: 3 residues within 4Å: Chain S: K.72 Chain T: Y.40, D.43 4 PLIP interactions: 1 interactions with chain S, 3 interactions with chain T Hydrogen bonds: S:K.72, T:Y.40, T:Y.40, T:D.43 GOL.80: 9 residues within 4Å: Chain B: D.132, E.135, T.136 Chain S: D.132, E.135, T.136 Chain U: D.132, E.135, T.136 4 PLIP interactions: 2 interactions with chain S, 1 interactions with chain U, 1 interactions with chain B Hydrogen bonds: S:E.135, S:T.136, B:T.136 Water bridges: U:T.136 GOL.88: 3 residues within 4Å: Chain L: Q.87, K.88 Chain W: D.85 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain W Hydrogen bonds: L:K.88, W:D.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunzle, M. et al., Binary Protein Crystals for the Assembly of Inorganic Nanoparticle Superlattices. J.Am.Chem.Soc. (2016)

Release Date

2016-10-26

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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