SMTL ID : 5z8u.1

Human mitochondrial ferritin mutant - C102A/C130A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-24-mer

Ligands

72 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.134 Chain C: E.134 Chain E: E.134 Ligands: MG.7, MG.13 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.27, A:E.62, A:H.65, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain B: E.134 Chain J: E.134 Chain X: E.134 Ligands: MG.27, MG.69 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.27, B:E.62, B:H.65, H2O.6, H2O.6 MG.5: 1 residues within 4Å: Chain B: D.84 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: D.84 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain A: E.134 Chain C: E.134 Chain E: E.134 Ligands: MG.1, MG.13 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain C: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.27, C:E.62, C:H.65, H2O.11, H2O.12 MG.9: 5 residues within 4Å: Chain D: E.134 Chain H: E.134 Chain R: E.134 Ligands: MG.21, MG.51 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain D: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.27, D:E.62, D:H.65, H2O.17, H2O.17 MG.11: 1 residues within 4Å: Chain D: D.84 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain C: D.84 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain A: E.134 Chain C: E.134 Chain E: E.134 Ligands: MG.1, MG.7 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain E: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.27, E:E.62, E:H.65, H2O.22, H2O.23 MG.15: 5 residues within 4Å: Chain F: E.134 Chain P: E.134 Chain T: E.134 Ligands: MG.45, MG.57 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain F: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.27, F:E.62, F:H.65, H2O.28, H2O.28 MG.17: 1 residues within 4Å: Chain F: D.84 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain E: D.84 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain G: E.134 Chain I: E.134 Chain K: E.134 Ligands: MG.25, MG.31 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain G: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.27, G:E.62, G:H.65, H2O.33, H2O.33 MG.21: 5 residues within 4Å: Chain D: E.134 Chain H: E.134 Chain R: E.134 Ligands: MG.9, MG.51 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain H: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.27, H:E.62, H:H.65, H2O.38, H2O.39 MG.23: 1 residues within 4Å: Chain H: D.84 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain G: D.84 No protein-ligand interaction detected (PLIP) MG.25: 5 residues within 4Å: Chain G: E.134 Chain I: E.134 Chain K: E.134 Ligands: MG.19, MG.31 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain I: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.27, I:E.62, I:H.65, H2O.44, H2O.44 MG.27: 5 residues within 4Å: Chain B: E.134 Chain J: E.134 Chain X: E.134 Ligands: MG.3, MG.69 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain J: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.27, J:E.62, J:H.65, H2O.49, H2O.49 MG.29: 1 residues within 4Å: Chain J: D.84 No protein-ligand interaction detected (PLIP) MG.30: 1 residues within 4Å: Chain I: D.84 No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain G: E.134 Chain I: E.134 Chain K: E.134 Ligands: MG.19, MG.25 No protein-ligand interaction detected (PLIP) MG.32: 4 residues within 4Å: Chain K: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.27, K:E.62, K:H.65, H2O.54, H2O.55 MG.33: 5 residues within 4Å: Chain L: E.134 Chain N: E.134 Chain V: E.134 Ligands: MG.39, MG.63 No protein-ligand interaction detected (PLIP) MG.34: 4 residues within 4Å: Chain L: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.27, L:E.62, L:H.65, H2O.60, H2O.60 MG.35: 1 residues within 4Å: Chain L: D.84 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain K: D.84 No protein-ligand interaction detected (PLIP) MG.37: 5 residues within 4Å: Chain M: E.134 Chain O: E.134 Chain Q: E.134 Ligands: MG.43, MG.49 No protein-ligand interaction detected (PLIP) MG.38: 4 residues within 4Å: Chain M: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.27, M:E.62, M:H.65, H2O.65, H2O.66 MG.39: 5 residues within 4Å: Chain L: E.134 Chain N: E.134 Chain V: E.134 Ligands: MG.33, MG.63 No protein-ligand interaction detected (PLIP) MG.40: 4 residues within 4Å: Chain N: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.27, N:E.62, N:H.65, H2O.71, H2O.71 MG.41: 1 residues within 4Å: Chain N: D.84 No protein-ligand interaction detected (PLIP) MG.42: 1 residues within 4Å: Chain M: D.84 No protein-ligand interaction detected (PLIP) MG.43: 5 residues within 4Å: Chain M: E.134 Chain O: E.134 Chain Q: E.134 Ligands: MG.37, MG.49 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain O: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain O, 2 Ligand-Water interactions Metal complexes: O:E.27, O:E.62, O:H.65, H2O.76, H2O.77 MG.45: 5 residues within 4Å: Chain F: E.134 Chain P: E.134 Chain T: E.134 Ligands: MG.15, MG.57 No protein-ligand interaction detected (PLIP) MG.46: 4 residues within 4Å: Chain P: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:E.27, P:E.62, P:H.65, H2O.81, H2O.82 MG.47: 1 residues within 4Å: Chain P: D.84 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Chain O: D.84 No protein-ligand interaction detected (PLIP) MG.49: 5 residues within 4Å: Chain M: E.134 Chain O: E.134 Chain Q: E.134 Ligands: MG.37, MG.43 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain Q: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain Q, 2 Ligand-Water interactions Metal complexes: Q:E.27, Q:E.62, Q:H.65, H2O.87, H2O.87 MG.51: 5 residues within 4Å: Chain D: E.134 Chain H: E.134 Chain R: E.134 Ligands: MG.9, MG.21 No protein-ligand interaction detected (PLIP) MG.52: 4 residues within 4Å: Chain R: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:E.27, R:E.62, R:H.65, H2O.92, H2O.93 MG.53: 1 residues within 4Å: Chain R: D.84 No protein-ligand interaction detected (PLIP) MG.54: 1 residues within 4Å: Chain Q: D.84 No protein-ligand interaction detected (PLIP) MG.55: 5 residues within 4Å: Chain S: E.134 Chain U: E.134 Chain W: E.134 Ligands: MG.61, MG.67 No protein-ligand interaction detected (PLIP) MG.56: 4 residues within 4Å: Chain S: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.27, S:E.62, S:H.65, H2O.98, H2O.98 MG.57: 5 residues within 4Å: Chain F: E.134 Chain P: E.134 Chain T: E.134 Ligands: MG.15, MG.45 No protein-ligand interaction detected (PLIP) MG.58: 4 residues within 4Å: Chain T: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.27, T:E.62, T:H.65, H2O.103, H2O.103 MG.59: 1 residues within 4Å: Chain T: D.84 No protein-ligand interaction detected (PLIP) MG.60: 1 residues within 4Å: Chain S: D.84 No protein-ligand interaction detected (PLIP) MG.61: 5 residues within 4Å: Chain S: E.134 Chain U: E.134 Chain W: E.134 Ligands: MG.55, MG.67 No protein-ligand interaction detected (PLIP) MG.62: 4 residues within 4Å: Chain U: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain U, 2 Ligand-Water interactions Metal complexes: U:E.27, U:E.62, U:H.65, H2O.108, H2O.109 MG.63: 5 residues within 4Å: Chain L: E.134 Chain N: E.134 Chain V: E.134 Ligands: MG.33, MG.39 No protein-ligand interaction detected (PLIP) MG.64: 4 residues within 4Å: Chain V: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.27, V:E.62, V:H.65, H2O.114, H2O.114 MG.65: 1 residues within 4Å: Chain V: D.84 No protein-ligand interaction detected (PLIP) MG.66: 1 residues within 4Å: Chain U: D.84 No protein-ligand interaction detected (PLIP) MG.67: 5 residues within 4Å: Chain S: E.134 Chain U: E.134 Chain W: E.134 Ligands: MG.55, MG.61 No protein-ligand interaction detected (PLIP) MG.68: 4 residues within 4Å: Chain W: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain W, 2 Ligand-Water interactions Metal complexes: W:E.27, W:E.62, W:H.65, H2O.119, H2O.120 MG.69: 5 residues within 4Å: Chain B: E.134 Chain J: E.134 Chain X: E.134 Ligands: MG.3, MG.27 No protein-ligand interaction detected (PLIP) MG.70: 4 residues within 4Å: Chain X: E.27, E.62, H.65, Q.141 5 PLIP interactions: 3 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:E.27, X:E.62, X:H.65, H2O.124, H2O.125 MG.71: 1 residues within 4Å: Chain X: D.84 No protein-ligand interaction detected (PLIP) MG.72: 1 residues within 4Å: Chain W: D.84 No protein-ligand interaction detected (PLIP)

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
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

M
A

N
B

O
A

P
B

Q
A

R
B

S
A

T
B

U
A

V
B

W
A

X
B

Ferritin, mitochondrial