SMTL ID : 5jkk.1

Crystal structure of the negatively supercharged variant Ftn(neg) of human heavy chain ferritin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-24-mer

Ligands

30 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: 5 residues within 4Å: Chain A: H.174 Chain C: H.174 Chain F: H.174 Chain G: H.174 Ligands: CL.5 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F, 1 interactions with chain G, 1 interactions with chain A Metal complexes: C:H.174, F:H.174, G:H.174, A:H.174 FE.6: 3 residues within 4Å: Chain B: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.28, B:E.63, B:H.66, H2O.9, H2O.10 FE.9: 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.18, H2O.19 FE.13: 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.26, H2O.26 FE.14: 5 residues within 4Å: Chain D: H.174 Chain E: H.174 Chain R: H.174 Chain X: H.174 Ligands: CL.17 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain X Metal complexes: R:H.174, D:H.174, E:H.174, X:H.174 FE.18: 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.34, H2O.34 FE.22: 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.41, H2O.43 FE.26: 3 residues within 4Å: Chain G: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.28, G:E.63, G:H.66, H2O.50, H2O.50 FE.28: 3 residues within 4Å: Chain H: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.28, H:E.63, H:H.66, H2O.58, H2O.58 FE.30: 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.66, H2O.66 FE.31: 5 residues within 4Å: Chain I: H.174 Chain K: H.174 Chain N: H.174 Chain O: H.174 Ligands: CL.34 4 PLIP interactions: 1 interactions with chain O, 1 interactions with chain I, 1 interactions with chain K, 1 interactions with chain N Metal complexes: O:H.174, I:H.174, K:H.174, N:H.174 FE.35: 3 residues within 4Å: Chain J: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.28, J:E.63, J:H.66, H2O.74, H2O.75 FE.38: 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.83, H2O.83 FE.42: 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.90, H2O.91 FE.43: 5 residues within 4Å: Chain B: H.174 Chain H: H.174 Chain L: H.174 Chain M: H.174 Ligands: CL.46 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain B, 1 interactions with chain H, 1 interactions with chain M Metal complexes: L:H.174, B:H.174, H:H.174, M: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.98, H2O.99 FE.51: 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.106, H2O.107 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.114, H2O.115 FE.57: 3 residues within 4Å: Chain P: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.28, P:E.63, P:H.66, H2O.123, H2O.123 FE.59: 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.130, H2O.131 FE.60: 5 residues within 4Å: Chain Q: H.174 Chain S: H.174 Chain V: H.174 Chain W: H.174 Ligands: CL.63 4 PLIP interactions: 1 interactions with chain S, 1 interactions with chain Q, 1 interactions with chain W, 1 interactions with chain V Metal complexes: S:H.174, Q:H.174, W:H.174, V:H.174 FE.64: 3 residues within 4Å: Chain R: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.28, R:E.63, R:H.66, H2O.138, H2O.139 FE.67: 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.147, H2O.148 FE.71: 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.155, H2O.155 FE.72: 5 residues within 4Å: Chain J: H.174 Chain P: H.174 Chain T: H.174 Chain U: H.174 Ligands: CL.75 4 PLIP interactions: 1 interactions with chain P, 1 interactions with chain T, 1 interactions with chain U, 1 interactions with chain J Metal complexes: P:H.174, T:H.174, U:H.174, J:H.174 FE.76: 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.163, H2O.163 FE.80: 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.171, H2O.172 FE.84: 3 residues within 4Å: Chain W: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.28, W:E.63, W:H.66, H2O.179, H2O.180 FE.86: 3 residues within 4Å: Chain X: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.28, X:E.63, X:H.66, H2O.187, H2O.188

51 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: Q.59 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: D.132 Chain I: D.132 Chain Q: D.132 Ligands: MG.33, MG.62 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: Q.59, E.62 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.62, H2O.9, H2O.10, H2O.12, H2O.16 MG.8: 3 residues within 4Å: Chain B: E.135 Chain C: E.135 Chain D: E.135 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: Q.59, E.62 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.62, H2O.18, H2O.20, H2O.20 MG.11: 3 residues within 4Å: Chain B: D.132 Chain C: D.132 Chain D: D.132 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain C: D.85 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.85, H2O.21, H2O.59 MG.15: 1 residues within 4Å: Chain D: Q.59 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain D: D.85 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.85, H2O.28, H2O.31 MG.19: 2 residues within 4Å: Chain E: Q.59, E.62 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.62, H2O.33, H2O.34, H2O.37 MG.20: 5 residues within 4Å: Chain E: E.135 Chain M: E.135 Chain U: E.135 Ligands: MG.49, MG.78 No protein-ligand interaction detected (PLIP) MG.21: 1 residues within 4Å: Chain E: D.85 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.85, H2O.10, H2O.37 MG.23: 1 residues within 4Å: Chain F: Q.59 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain F: E.135 Chain H: E.135 Chain O: E.135 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain F: D.85 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.85, H2O.42, H2O.47 MG.27: 1 residues within 4Å: Chain G: Q.59 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain H: Q.59, E.62 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.62, H2O.57, H2O.57 MG.32: 1 residues within 4Å: Chain I: Q.59 No protein-ligand interaction detected (PLIP) MG.33: 5 residues within 4Å: Chain A: D.132 Chain I: D.132 Chain Q: D.132 Ligands: MG.4, MG.62 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain J: Q.59, E.62 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:E.62, H2O.73, H2O.75, H2O.77, H2O.80 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.39: 2 residues within 4Å: Chain K: Q.59, E.62 4 PLIP interactions: 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:E.62, H2O.82, H2O.85, H2O.85 MG.40: 3 residues within 4Å: Chain J: D.132 Chain K: D.132 Chain L: D.132 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain K: D.85 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:D.85, H2O.86, H2O.123 MG.44: 1 residues within 4Å: Chain L: Q.59 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Chain L: D.85 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.85, H2O.93, H2O.96 MG.48: 2 residues within 4Å: Chain M: Q.59, E.62 4 PLIP interactions: 1 interactions with chain M, 3 Ligand-Water interactions Metal complexes: M:E.62, H2O.98, H2O.98, H2O.102 MG.49: 5 residues within 4Å: Chain E: E.135 Chain M: E.135 Chain U: E.135 Ligands: MG.20, MG.78 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain M: D.85 3 PLIP interactions: 1 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:D.85, H2O.74, H2O.102 MG.52: 1 residues within 4Å: Chain N: Q.59 No protein-ligand interaction detected (PLIP) MG.53: 3 residues within 4Å: Chain N: E.135 Chain P: E.135 Chain W: E.135 No protein-ligand interaction detected (PLIP) MG.54: 1 residues within 4Å: Chain N: D.85 3 PLIP interactions: 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:D.85, H2O.107, H2O.112 MG.56: 1 residues within 4Å: Chain O: Q.59 No protein-ligand interaction detected (PLIP) MG.58: 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.122, H2O.122 MG.61: 1 residues within 4Å: Chain Q: Q.59 No protein-ligand interaction detected (PLIP) MG.62: 5 residues within 4Å: Chain A: D.132 Chain I: D.132 Chain Q: D.132 Ligands: MG.4, MG.33 No protein-ligand interaction detected (PLIP) MG.65: 2 residues within 4Å: Chain R: Q.59, E.62 5 PLIP interactions: 1 interactions with chain R, 4 Ligand-Water interactions Metal complexes: R:E.62, H2O.138, H2O.139, H2O.141, H2O.145 MG.66: 3 residues within 4Å: Chain R: E.135 Chain S: E.135 Chain T: E.135 No protein-ligand interaction detected (PLIP) MG.68: 2 residues within 4Å: Chain S: Q.59, E.62 4 PLIP interactions: 1 interactions with chain S, 3 Ligand-Water interactions Metal complexes: S:E.62, H2O.147, H2O.150, H2O.150 MG.69: 3 residues within 4Å: Chain R: D.132 Chain S: D.132 Chain T: D.132 No protein-ligand interaction detected (PLIP) MG.70: 1 residues within 4Å: Chain S: D.85 3 PLIP interactions: 1 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:D.85, H2O.150, H2O.188 MG.73: 1 residues within 4Å: Chain T: Q.59 No protein-ligand interaction detected (PLIP) MG.74: 1 residues within 4Å: Chain T: D.85 3 PLIP interactions: 1 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:D.85, H2O.157, H2O.160 MG.77: 2 residues within 4Å: Chain U: Q.59, E.62 4 PLIP interactions: 1 interactions with chain U, 3 Ligand-Water interactions Metal complexes: U:E.62, H2O.163, H2O.163, H2O.167 MG.78: 5 residues within 4Å: Chain E: E.135 Chain M: E.135 Chain U: E.135 Ligands: MG.20, MG.49 No protein-ligand interaction detected (PLIP) MG.79: 1 residues within 4Å: Chain U: D.85 3 PLIP interactions: 1 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:D.85, H2O.139, H2O.167 MG.81: 1 residues within 4Å: Chain V: Q.59 No protein-ligand interaction detected (PLIP) MG.82: 3 residues within 4Å: Chain G: E.135 Chain V: E.135 Chain X: E.135 No protein-ligand interaction detected (PLIP) MG.83: 1 residues within 4Å: Chain V: D.85 3 PLIP interactions: 1 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:D.85, H2O.172, H2O.176 MG.85: 1 residues within 4Å: Chain W: Q.59 No protein-ligand interaction detected (PLIP) MG.87: 2 residues within 4Å: Chain X: Q.59, E.62 3 PLIP interactions: 1 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.62, H2O.186, H2O.187

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

CL.5: 9 residues within 4Å: Chain A: L.170, H.174 Chain C: L.170, H.174 Chain F: L.170, H.174 Chain G: L.170, H.174 Ligands: FE.2 Ligand excluded by PLIP CL.17: 9 residues within 4Å: Chain D: L.170, H.174 Chain E: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: FE.14 Ligand excluded by PLIP CL.34: 9 residues within 4Å: Chain I: L.170, H.174 Chain K: L.170, H.174 Chain N: L.170, H.174 Chain O: L.170, H.174 Ligands: FE.31 Ligand excluded by PLIP CL.46: 9 residues within 4Å: Chain B: L.170, H.174 Chain H: L.170, H.174 Chain L: L.170, H.174 Chain M: L.170, H.174 Ligands: FE.43 Ligand excluded by PLIP CL.63: 9 residues within 4Å: Chain Q: L.170, H.174 Chain S: L.170, H.174 Chain V: L.170, H.174 Chain W: L.170, H.174 Ligands: FE.60 Ligand excluded by PLIP CL.75: 9 residues within 4Å: Chain J: L.170, H.174 Chain P: L.170, H.174 Chain T: L.170, H.174 Chain U: L.170, H.174 Ligands: FE.72 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunzle, M. et al., Metal-Assisted Assembly of Protein Containers Loaded with Inorganic Nanoparticles. Inorg.Chem. (2018)

Release Date

2017-05-10

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
G

H
H

I
A

J
B

K
C

L
D

M
E

N
F

O
G

P
H

Q
A

R
B

S
C

T
D

U
E

V
F

W
G

X
H

Ferritin heavy chain

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