SMTL ID : 5z91.1

Human mitochondrial ferritin mutant bound with gold ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-24-mer

Ligands

48 x AU: GOLD ION(Non-covalent)

AU.1: 5 residues within 4Å: Chain A: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.2: 2 residues within 4Å: Chain A: H.98, C.102 Ligand excluded by PLIP AU.5: 5 residues within 4Å: Chain B: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.6: 2 residues within 4Å: Chain B: H.98, C.102 Ligand excluded by PLIP AU.9: 5 residues within 4Å: Chain C: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.10: 2 residues within 4Å: Chain C: H.98, C.102 Ligand excluded by PLIP AU.13: 5 residues within 4Å: Chain D: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.14: 2 residues within 4Å: Chain D: H.98, C.102 Ligand excluded by PLIP AU.17: 5 residues within 4Å: Chain E: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.18: 2 residues within 4Å: Chain E: H.98, C.102 Ligand excluded by PLIP AU.21: 5 residues within 4Å: Chain F: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.22: 2 residues within 4Å: Chain F: H.98, C.102 Ligand excluded by PLIP AU.25: 5 residues within 4Å: Chain G: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.26: 2 residues within 4Å: Chain G: H.98, C.102 Ligand excluded by PLIP AU.29: 5 residues within 4Å: Chain H: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.30: 2 residues within 4Å: Chain H: H.98, C.102 Ligand excluded by PLIP AU.33: 5 residues within 4Å: Chain I: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.34: 2 residues within 4Å: Chain I: H.98, C.102 Ligand excluded by PLIP AU.37: 5 residues within 4Å: Chain J: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.38: 2 residues within 4Å: Chain J: H.98, C.102 Ligand excluded by PLIP AU.41: 5 residues within 4Å: Chain K: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.42: 2 residues within 4Å: Chain K: H.98, C.102 Ligand excluded by PLIP AU.45: 5 residues within 4Å: Chain L: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.46: 2 residues within 4Å: Chain L: H.98, C.102 Ligand excluded by PLIP AU.49: 5 residues within 4Å: Chain M: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.50: 2 residues within 4Å: Chain M: H.98, C.102 Ligand excluded by PLIP AU.53: 5 residues within 4Å: Chain N: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.54: 2 residues within 4Å: Chain N: H.98, C.102 Ligand excluded by PLIP AU.57: 5 residues within 4Å: Chain O: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.58: 2 residues within 4Å: Chain O: H.98, C.102 Ligand excluded by PLIP AU.61: 5 residues within 4Å: Chain P: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.62: 2 residues within 4Å: Chain P: H.98, C.102 Ligand excluded by PLIP AU.65: 5 residues within 4Å: Chain Q: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.66: 2 residues within 4Å: Chain Q: H.98, C.102 Ligand excluded by PLIP AU.69: 5 residues within 4Å: Chain R: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.70: 2 residues within 4Å: Chain R: H.98, C.102 Ligand excluded by PLIP AU.73: 5 residues within 4Å: Chain S: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.74: 2 residues within 4Å: Chain S: H.98, C.102 Ligand excluded by PLIP AU.77: 5 residues within 4Å: Chain T: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.78: 2 residues within 4Å: Chain T: H.98, C.102 Ligand excluded by PLIP AU.81: 5 residues within 4Å: Chain U: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.82: 2 residues within 4Å: Chain U: H.98, C.102 Ligand excluded by PLIP AU.85: 5 residues within 4Å: Chain V: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.86: 2 residues within 4Å: Chain V: H.98, C.102 Ligand excluded by PLIP AU.89: 5 residues within 4Å: Chain W: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.90: 2 residues within 4Å: Chain W: H.98, C.102 Ligand excluded by PLIP AU.93: 5 residues within 4Å: Chain X: A.121, S.122, D.126, P.127, C.130 Ligand excluded by PLIP AU.94: 2 residues within 4Å: Chain X: H.98, C.102 Ligand excluded by PLIP

48 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: H.173 Chain C: H.173 Chain U: H.173 Chain W: H.173 Ligands: MG.11, MG.83, MG.91 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain C, 1 interactions with chain A Metal complexes: U:H.173, W:H.173, C:H.173, A:H.173 MG.4: 5 residues within 4Å: Chain A: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.27, A:E.27, A:E.62, A:E.62, A:H.65 MG.7: 7 residues within 4Å: Chain B: H.173 Chain D: H.173 Chain V: H.173 Chain X: H.173 Ligands: MG.15, MG.87, MG.95 4 PLIP interactions: 1 interactions with chain V, 1 interactions with chain X, 1 interactions with chain B, 1 interactions with chain D Metal complexes: V:H.173, X:H.173, B:H.173, D:H.173 MG.8: 5 residues within 4Å: Chain B: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.27, B:E.27, B:E.62, B:E.62, B:H.65 MG.11: 7 residues within 4Å: Chain A: H.173 Chain C: H.173 Chain U: H.173 Chain W: H.173 Ligands: MG.3, MG.83, MG.91 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain W, 1 interactions with chain C, 1 interactions with chain A Metal complexes: U:H.173, W:H.173, C:H.173, A:H.173 MG.12: 5 residues within 4Å: Chain C: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.27, C:E.27, C:E.62, C:E.62, C:H.65 MG.15: 7 residues within 4Å: Chain B: H.173 Chain D: H.173 Chain V: H.173 Chain X: H.173 Ligands: MG.7, MG.87, MG.95 4 PLIP interactions: 1 interactions with chain V, 1 interactions with chain X, 1 interactions with chain B, 1 interactions with chain D Metal complexes: V:H.173, X:H.173, B:H.173, D:H.173 MG.16: 5 residues within 4Å: Chain D: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.27, D:E.27, D:E.62, D:E.62, D:H.65 MG.19: 7 residues within 4Å: Chain E: H.173 Chain G: H.173 Chain R: H.173 Chain T: H.173 Ligands: MG.27, MG.71, MG.79 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 1 interactions with chain T, 1 interactions with chain R Metal complexes: E:H.173, G:H.173, T:H.173, R:H.173 MG.20: 5 residues within 4Å: Chain E: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.27, E:E.27, E:E.62, E:E.62, E:H.65 MG.23: 7 residues within 4Å: Chain F: H.173 Chain H: H.173 Chain Q: H.173 Chain S: H.173 Ligands: MG.31, MG.67, MG.75 4 PLIP interactions: 1 interactions with chain S, 1 interactions with chain Q, 1 interactions with chain H, 1 interactions with chain F Metal complexes: S:H.173, Q:H.173, H:H.173, F:H.173 MG.24: 5 residues within 4Å: Chain F: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.27, F:E.27, F:E.62, F:E.62, F:H.65 MG.27: 7 residues within 4Å: Chain E: H.173 Chain G: H.173 Chain R: H.173 Chain T: H.173 Ligands: MG.19, MG.71, MG.79 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 1 interactions with chain T, 1 interactions with chain R Metal complexes: E:H.173, G:H.173, T:H.173, R:H.173 MG.28: 5 residues within 4Å: Chain G: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.27, G:E.27, G:E.62, G:E.62, G:H.65 MG.31: 7 residues within 4Å: Chain F: H.173 Chain H: H.173 Chain Q: H.173 Chain S: H.173 Ligands: MG.23, MG.67, MG.75 4 PLIP interactions: 1 interactions with chain S, 1 interactions with chain Q, 1 interactions with chain H, 1 interactions with chain F Metal complexes: S:H.173, Q:H.173, H:H.173, F:H.173 MG.32: 5 residues within 4Å: Chain H: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.27, H:E.27, H:E.62, H:E.62, H:H.65 MG.35: 7 residues within 4Å: Chain I: H.173 Chain K: H.173 Chain M: H.173 Chain O: H.173 Ligands: MG.43, MG.51, MG.59 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I, 1 interactions with chain M, 1 interactions with chain O Metal complexes: K:H.173, I:H.173, M:H.173, O:H.173 MG.36: 5 residues within 4Å: Chain I: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.27, I:E.27, I:E.62, I:E.62, I:H.65 MG.39: 7 residues within 4Å: Chain J: H.173 Chain L: H.173 Chain N: H.173 Chain P: H.173 Ligands: MG.47, MG.55, MG.63 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain J, 1 interactions with chain P, 1 interactions with chain N Metal complexes: L:H.173, J:H.173, P:H.173, N:H.173 MG.40: 5 residues within 4Å: Chain J: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.27, J:E.27, J:E.62, J:E.62, J:H.65 MG.43: 7 residues within 4Å: Chain I: H.173 Chain K: H.173 Chain M: H.173 Chain O: H.173 Ligands: MG.35, MG.51, MG.59 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I, 1 interactions with chain M, 1 interactions with chain O Metal complexes: K:H.173, I:H.173, M:H.173, O:H.173 MG.44: 5 residues within 4Å: Chain K: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:E.27, K:E.27, K:E.62, K:E.62, K:H.65 MG.47: 7 residues within 4Å: Chain J: H.173 Chain L: H.173 Chain N: H.173 Chain P: H.173 Ligands: MG.39, MG.55, MG.63 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain J, 1 interactions with chain P, 1 interactions with chain N Metal complexes: L:H.173, J:H.173, P:H.173, N:H.173 MG.48: 5 residues within 4Å: Chain L: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:E.27, L:E.27, L:E.62, L:E.62, L:H.65 MG.51: 7 residues within 4Å: Chain I: H.173 Chain K: H.173 Chain M: H.173 Chain O: H.173 Ligands: MG.35, MG.43, MG.59 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I, 1 interactions with chain M, 1 interactions with chain O Metal complexes: K:H.173, I:H.173, M:H.173, O:H.173 MG.52: 5 residues within 4Å: Chain M: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:E.27, M:E.27, M:E.62, M:E.62, M:H.65 MG.55: 7 residues within 4Å: Chain J: H.173 Chain L: H.173 Chain N: H.173 Chain P: H.173 Ligands: MG.39, MG.47, MG.63 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain J, 1 interactions with chain P, 1 interactions with chain N Metal complexes: L:H.173, J:H.173, P:H.173, N:H.173 MG.56: 5 residues within 4Å: Chain N: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:E.27, N:E.27, N:E.62, N:E.62, N:H.65 MG.59: 7 residues within 4Å: Chain I: H.173 Chain K: H.173 Chain M: H.173 Chain O: H.173 Ligands: MG.35, MG.43, MG.51 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I, 1 interactions with chain M, 1 interactions with chain O Metal complexes: K:H.173, I:H.173, M:H.173, O:H.173 MG.60: 5 residues within 4Å: Chain O: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:E.27, O:E.27, O:E.62, O:E.62, O:H.65 MG.63: 7 residues within 4Å: Chain J: H.173 Chain L: H.173 Chain N: H.173 Chain P: H.173 Ligands: MG.39, MG.47, MG.55 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain N, 1 interactions with chain P, 1 interactions with chain L Metal complexes: J:H.173, N:H.173, P:H.173, L:H.173 MG.64: 5 residues within 4Å: Chain P: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:E.27, P:E.27, P:E.62, P:E.62, P:H.65 MG.67: 7 residues within 4Å: Chain F: H.173 Chain H: H.173 Chain Q: H.173 Chain S: H.173 Ligands: MG.23, MG.31, MG.75 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain Q, 1 interactions with chain H, 1 interactions with chain S Metal complexes: F:H.173, Q:H.173, H:H.173, S:H.173 MG.68: 5 residues within 4Å: Chain Q: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain Q Metal complexes: Q:E.27, Q:E.27, Q:E.62, Q:E.62, Q:H.65 MG.71: 7 residues within 4Å: Chain E: H.173 Chain G: H.173 Chain R: H.173 Chain T: H.173 Ligands: MG.19, MG.27, MG.79 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain R, 1 interactions with chain T, 1 interactions with chain G Metal complexes: E:H.173, R:H.173, T:H.173, G:H.173 MG.72: 5 residues within 4Å: Chain R: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:E.27, R:E.27, R:E.62, R:E.62, R:H.65 MG.75: 7 residues within 4Å: Chain F: H.173 Chain H: H.173 Chain Q: H.173 Chain S: H.173 Ligands: MG.23, MG.31, MG.67 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain Q, 1 interactions with chain H, 1 interactions with chain S Metal complexes: F:H.173, Q:H.173, H:H.173, S:H.173 MG.76: 5 residues within 4Å: Chain S: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:E.27, S:E.27, S:E.62, S:E.62, S:H.65 MG.79: 7 residues within 4Å: Chain E: H.173 Chain G: H.173 Chain R: H.173 Chain T: H.173 Ligands: MG.19, MG.27, MG.71 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain R, 1 interactions with chain T, 1 interactions with chain G Metal complexes: E:H.173, R:H.173, T:H.173, G:H.173 MG.80: 5 residues within 4Å: Chain T: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain T Metal complexes: T:E.27, T:E.27, T:E.62, T:E.62, T:H.65 MG.83: 7 residues within 4Å: Chain A: H.173 Chain C: H.173 Chain U: H.173 Chain W: H.173 Ligands: MG.3, MG.11, MG.91 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain W, 1 interactions with chain C, 1 interactions with chain U Metal complexes: A:H.173, W:H.173, C:H.173, U:H.173 MG.84: 5 residues within 4Å: Chain U: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain U Metal complexes: U:E.27, U:E.27, U:E.62, U:E.62, U:H.65 MG.87: 7 residues within 4Å: Chain B: H.173 Chain D: H.173 Chain V: H.173 Chain X: H.173 Ligands: MG.7, MG.15, MG.95 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain V, 1 interactions with chain D, 1 interactions with chain B Metal complexes: X:H.173, V:H.173, D:H.173, B:H.173 MG.88: 5 residues within 4Å: Chain V: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain V Metal complexes: V:E.27, V:E.27, V:E.62, V:E.62, V:H.65 MG.91: 7 residues within 4Å: Chain A: H.173 Chain C: H.173 Chain U: H.173 Chain W: H.173 Ligands: MG.3, MG.11, MG.83 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain W, 1 interactions with chain C, 1 interactions with chain U Metal complexes: A:H.173, W:H.173, C:H.173, U:H.173 MG.92: 5 residues within 4Å: Chain W: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain W Metal complexes: W:E.27, W:E.27, W:E.62, W:E.62, W:H.65 MG.95: 7 residues within 4Å: Chain B: H.173 Chain D: H.173 Chain V: H.173 Chain X: H.173 Ligands: MG.7, MG.15, MG.87 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain X, 1 interactions with chain B, 1 interactions with chain V Metal complexes: D:H.173, X:H.173, B:H.173, V:H.173 MG.96: 5 residues within 4Å: Chain X: E.27, E.62, H.65, V.110, Q.141 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:E.27, X:E.27, X:E.62, X:E.62, X:H.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zang, J. et al., Design and site-directed compartmentalization of gold nanoclusters within the intrasubunit interfaces of ferritin nanocage. J Nanobiotechnology (2019)

Release Date

2019-02-06

Peptides

Ferritin, mitochondrial: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

M
A

N
A

O
A

P
A

Q
A

R
A

S
A

T
A

U
A

V
A

W
A

X
A

Ferritin, mitochondrial

Related Entries With Identical Sequence