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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 3 residues within 4Å: Chain A: E.28, E.63, H.66 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.5: 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.6, H2O.6 FE.7: 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.12, H2O.13 FE.9: 3 residues within 4Å: Chain D: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.28, D:E.63, D:H.66, H2O.18, H2O.18 FE.12: 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.23, H2O.24 FE.15: 3 residues within 4Å: Chain F: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.28, F:E.63, F:H.66, H2O.28, H2O.30 FE.17: 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.33, H2O.34 FE.21: 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.39, H2O.39 FE.23: 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.45, H2O.45 FE.25: 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.51, H2O.51 FE.28: 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.56, H2O.56 FE.31: 3 residues within 4Å: Chain L: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.28, L:E.63, L:H.66, H2O.61, H2O.62 FE.33: 3 residues within 4Å: Chain M: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.28, M:E.63, M:H.66, H2O.66, H2O.66 FE.37: 3 residues within 4Å: Chain N: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.28, N:E.63, N:H.66, H2O.72, H2O.72 FE.39: 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.78, H2O.78 FE.41: 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.84, H2O.84 FE.44: 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.89, H2O.89 FE.47: 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.94, H2O.95 FE.49: 3 residues within 4Å: Chain S: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.28, S:E.63, S:H.66, H2O.99, H2O.99 FE.53: 3 residues within 4Å: Chain T: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:E.28, T:E.63, T:H.66, H2O.104, H2O.104 FE.55: 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.110, H2O.110 FE.57: 3 residues within 4Å: Chain V: E.28, E.63, H.66 5 PLIP interactions: 3 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:E.28, V:E.63, V:H.66, H2O.116, H2O.116 FE.60: 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.121, H2O.121 FE.63: 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.126, H2O.127

32 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.135 Chain C: E.135 Chain N: E.135 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: Q.59 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: Q.59, E.62 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.62 MG.8: 3 residues within 4Å: Chain C: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain D: E.135 Chain E: E.135 Chain F: E.135 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain D: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain D: D.132 Chain E: D.132 Chain F: D.132 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain F: Q.59, E.62, E.63 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.62 MG.18: 3 residues within 4Å: Chain G: E.135 Chain I: E.135 Chain T: E.135 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain G: Q.59 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain H: Q.59, E.62 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.62 MG.24: 3 residues within 4Å: Chain I: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain J: E.135 Chain K: E.135 Chain L: E.135 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain J: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain J: D.132 Chain K: D.132 Chain L: D.132 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain L: Q.59, E.62, E.63 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.62 MG.34: 3 residues within 4Å: Chain H: E.135 Chain M: E.135 Chain O: E.135 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain M: Q.59 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain N: Q.59, E.62 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.62 MG.40: 3 residues within 4Å: Chain O: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain P: E.135 Chain Q: E.135 Chain R: E.135 No protein-ligand interaction detected (PLIP) MG.43: 4 residues within 4Å: Chain P: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.45: 3 residues within 4Å: Chain P: D.132 Chain Q: D.132 Chain R: D.132 No protein-ligand interaction detected (PLIP) MG.48: 3 residues within 4Å: Chain R: Q.59, E.62, E.63 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.62 MG.50: 3 residues within 4Å: Chain B: E.135 Chain S: E.135 Chain U: E.135 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain S: Q.59 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain T: Q.59, E.62 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:E.62 MG.56: 3 residues within 4Å: Chain U: Q.59, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.58: 3 residues within 4Å: Chain V: E.135 Chain W: E.135 Chain X: E.135 No protein-ligand interaction detected (PLIP) MG.59: 4 residues within 4Å: Chain V: Q.59, E.62, E.63, E.108 No protein-ligand interaction detected (PLIP) MG.61: 3 residues within 4Å: Chain V: D.132 Chain W: D.132 Chain X: D.132 No protein-ligand interaction detected (PLIP) MG.64: 3 residues within 4Å: Chain X: Q.59, E.62, E.63 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:E.62

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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 5 PLIP interactions: 1 interactions with chain N, 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: N:D.132, A:D.132, A:E.135, C:E.135, C:T.136 GOL.14: 3 residues within 4Å: Chain E: D.85 Chain X: Q.87, K.88 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.85 GOL.20: 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 5 PLIP interactions: 1 interactions with chain T, 2 interactions with chain G, 2 interactions with chain I Hydrogen bonds: T:D.132, G:D.132, G:E.135, I:E.135, I:T.136 GOL.30: 3 residues within 4Å: Chain K: D.85 Chain R: Q.87, K.88 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.85 GOL.36: 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 5 PLIP interactions: 2 interactions with chain M, 2 interactions with chain O, 1 interactions with chain H Hydrogen bonds: M:D.132, M:E.135, O:E.135, O:T.136, H:D.132 GOL.46: 3 residues within 4Å: Chain F: Q.87, K.88 Chain Q: D.85 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:D.85 GOL.52: 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 5 PLIP interactions: 2 interactions with chain U, 2 interactions with chain S, 1 interactions with chain B Hydrogen bonds: U:E.135, U:T.136, S:D.132, S:E.135, B:D.132 GOL.62: 3 residues within 4Å: Chain L: Q.87, K.88 Chain W: D.85 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: 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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