SMTL ID : 5jkl.2 (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.2 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.20, CL.23, FE.38, CL.41, FE.56, CL.59 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain G, 1 interactions with chain S, 1 interactions with chain A Metal complexes: M:H.174, G: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.7: 5 residues within 4Å: Chain B: H.174 Chain C: H.174 Chain D: H.174 Chain E: H.174 Ligands: CL.9 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Metal complexes: E:H.174, D:H.174, B:H.174, C:H.174 FE.10: 4 residues within 4Å: Chain C: E.28, E.63, H.66, 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.10, H2O.10 FE.11: 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.13, H2O.14 FE.13: 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.18, H2O.18 FE.15: 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.21, H2O.21 FE.16: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: CL.18, FE.34, CL.36, FE.52, CL.54, FE.70, CL.72 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.19: 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.24, H2O.26 FE.20: 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.23, FE.38, CL.41, FE.56, CL.59 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain M, 1 interactions with chain A, 1 interactions with chain S Metal complexes: G:H.174, M:H.174, A:H.174, S:H.174 FE.24: 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.29, H2O.31 FE.25: 5 residues within 4Å: Chain H: H.174 Chain I: H.174 Chain J: H.174 Chain K: H.174 Ligands: CL.27 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I, 1 interactions with chain H, 1 interactions with chain K Metal complexes: J:H.174, I:H.174, H:H.174, K:H.174 FE.28: 4 residues within 4Å: Chain I: E.28, E.63, H.66, 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.33, H2O.34 FE.29: 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.37, H2O.38 FE.31: 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.41, H2O.42 FE.33: 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.45, H2O.45 FE.34: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.16, CL.18, CL.36, FE.52, CL.54, FE.70, CL.72 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain X, 1 interactions with chain R, 1 interactions with chain F Metal complexes: L:H.174, X:H.174, R:H.174, F:H.174 FE.37: 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.48, H2O.49 FE.38: 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.20, CL.23, CL.41, FE.56, CL.59 4 PLIP interactions: 1 interactions with chain S, 1 interactions with chain M, 1 interactions with chain G, 1 interactions with chain A Metal complexes: S:H.174, M:H.174, G:H.174, A:H.174 FE.42: 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.53, H2O.54 FE.43: 5 residues within 4Å: Chain N: H.174 Chain O: H.174 Chain P: H.174 Chain Q: H.174 Ligands: CL.45 4 PLIP interactions: 1 interactions with chain P, 1 interactions with chain Q, 1 interactions with chain O, 1 interactions with chain N Metal complexes: P:H.174, Q:H.174, O:H.174, N:H.174 FE.46: 4 residues within 4Å: Chain O: E.28, E.63, H.66, 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.57, H2O.58 FE.47: 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.61, H2O.62 FE.49: 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.65, H2O.66 FE.51: 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.68, H2O.69 FE.52: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.16, CL.18, FE.34, CL.36, CL.54, FE.70, CL.72 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 FE.55: 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.72, H2O.73 FE.56: 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.20, CL.23, FE.38, CL.41, CL.59 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain S, 1 interactions with chain M, 1 interactions with chain G Metal complexes: A:H.174, S:H.174, M:H.174, G:H.174 FE.60: 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.77, H2O.78 FE.61: 5 residues within 4Å: Chain T: H.174 Chain U: H.174 Chain V: H.174 Chain W: H.174 Ligands: CL.63 4 PLIP interactions: 1 interactions with chain V, 1 interactions with chain T, 1 interactions with chain W, 1 interactions with chain U Metal complexes: V:H.174, T:H.174, W:H.174, U:H.174 FE.64: 4 residues within 4Å: Chain U: E.28, E.63, H.66, 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.81, H2O.81 FE.65: 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.85, H2O.85 FE.67: 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.89, H2O.89 FE.69: 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.92, H2O.93 FE.70: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.16, CL.18, FE.34, CL.36, FE.52, CL.54, CL.72 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain F, 1 interactions with chain L, 1 interactions with chain X Metal complexes: R:H.174, F:H.174, L:H.174, X:H.174

24 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.132 Chain C: D.132, E.135 Chain T: D.132 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: E.135 Chain C: E.135 Chain T: E.135 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: Q.59, E.62 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.62, H2O.5, H2O.5, H2O.7 MG.12: 3 residues within 4Å: Chain D: E.135 Chain F: E.135 Chain Q: E.135 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain E: Q.59, E.62 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.62, H2O.17, H2O.17 MG.17: 1 residues within 4Å: Chain F: Q.59 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain G: D.132 Chain I: D.132, E.135 Chain N: D.132 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain G: E.135 Chain I: E.135 Chain N: E.135 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain H: Q.59, E.62 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:E.62, H2O.29, H2O.29, H2O.30 MG.30: 3 residues within 4Å: Chain J: E.135 Chain L: E.135 Chain W: E.135 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain K: Q.59, E.62 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.62, H2O.41, H2O.41 MG.35: 1 residues within 4Å: Chain L: Q.59 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain B: D.132 Chain M: D.132 Chain O: D.132, E.135 No protein-ligand interaction detected (PLIP) MG.40: 3 residues within 4Å: Chain B: E.135 Chain M: E.135 Chain O: E.135 No protein-ligand interaction detected (PLIP) MG.44: 2 residues within 4Å: Chain N: Q.59, E.62 4 PLIP interactions: 1 interactions with chain N, 3 Ligand-Water interactions Metal complexes: N:E.62, H2O.53, H2O.53, H2O.54 MG.48: 3 residues within 4Å: Chain K: E.135 Chain P: E.135 Chain R: E.135 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain Q: Q.59, E.62 3 PLIP interactions: 1 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.62, H2O.65, H2O.65 MG.53: 1 residues within 4Å: Chain R: Q.59 No protein-ligand interaction detected (PLIP) MG.57: 4 residues within 4Å: Chain H: D.132 Chain S: D.132 Chain U: D.132, E.135 No protein-ligand interaction detected (PLIP) MG.58: 3 residues within 4Å: Chain H: E.135 Chain S: E.135 Chain U: E.135 No protein-ligand interaction detected (PLIP) MG.62: 2 residues within 4Å: Chain T: Q.59, E.62 4 PLIP interactions: 1 interactions with chain T, 3 Ligand-Water interactions Metal complexes: T:E.62, H2O.76, H2O.77, H2O.78 MG.66: 3 residues within 4Å: Chain E: E.135 Chain V: E.135 Chain X: E.135 No protein-ligand interaction detected (PLIP) MG.68: 2 residues within 4Å: Chain W: Q.59, E.62 3 PLIP interactions: 1 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.62, H2O.89, H2O.89 MG.71: 1 residues within 4Å: Chain X: Q.59 No protein-ligand interaction detected (PLIP)

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

CL.5: 11 residues within 4Å: Chain A: H.174 Chain G: H.174 Chain M: H.174 Chain S: H.174 Ligands: FE.2, FE.20, CL.23, FE.38, CL.41, FE.56, CL.59 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain B: H.174 Chain C: L.170, H.174 Chain D: L.170, H.174 Chain E: H.174 Ligands: FE.7 Ligand excluded by PLIP CL.18: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.16, FE.34, CL.36, FE.52, CL.54, FE.70, CL.72 Ligand excluded by PLIP CL.23: 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.20, FE.38, CL.41, FE.56, CL.59 Ligand excluded by PLIP CL.27: 7 residues within 4Å: Chain H: H.174 Chain I: L.170, H.174 Chain J: L.170, H.174 Chain K: H.174 Ligands: FE.25 Ligand excluded by PLIP CL.36: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.16, CL.18, FE.34, FE.52, CL.54, FE.70, CL.72 Ligand excluded by PLIP CL.41: 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.20, CL.23, FE.38, FE.56, CL.59 Ligand excluded by PLIP CL.45: 7 residues within 4Å: Chain N: H.174 Chain O: L.170, H.174 Chain P: L.170, H.174 Chain Q: H.174 Ligands: FE.43 Ligand excluded by PLIP CL.54: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.16, CL.18, FE.34, CL.36, FE.52, FE.70, CL.72 Ligand excluded by PLIP CL.59: 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.20, CL.23, FE.38, CL.41, FE.56 Ligand excluded by PLIP CL.63: 7 residues within 4Å: Chain T: H.174 Chain U: L.170, H.174 Chain V: L.170, H.174 Chain W: H.174 Ligands: FE.61 Ligand excluded by PLIP CL.72: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: FE.16, CL.18, FE.34, CL.36, FE.52, CL.54, FE.70 Ligand excluded by PLIP

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
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

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