SMTL ID : 5jkm.2 (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 Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-24-mer

Ligands

24 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.5: 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.7, H2O.7 FE.7: 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.11 FE.9: 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.14, H2O.15 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.18, H2O.19 FE.14: 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.22, H2O.23 FE.16: 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.27, H2O.27 FE.20: 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.32, H2O.33 FE.22: 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.36, H2O.37 FE.24: 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.40, H2O.41 FE.27: 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.44, H2O.44 FE.29: 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.48, H2O.49 FE.31: 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.53, H2O.53 FE.35: 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.58, H2O.59 FE.37: 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.61, H2O.62 FE.39: 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.65, H2O.66 FE.42: 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.70, H2O.70 FE.44: 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.74, H2O.75 FE.46: 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.78, H2O.78 FE.50: 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.83, H2O.84 FE.52: 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.87, H2O.88 FE.54: 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.91, H2O.92 FE.57: 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.95, H2O.95 FE.59: 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.99, H2O.100

36 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.132 Chain C: D.132 Chain T: D.132, E.135 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: E.135 Chain C: E.135 Chain T: E.135 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: Q.59, E.62 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: Q.59, E.62 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.62, H2O.5 MG.8: 3 residues within 4Å: Chain C: Q.59, E.62, E.63 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.62, H2O.11 MG.10: 3 residues within 4Å: Chain D: E.135 Chain F: E.135 Chain Q: E.135 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain D: Q.59, E.62 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.62 MG.13: 2 residues within 4Å: Chain E: Q.59, E.62 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.62 MG.15: 2 residues within 4Å: Chain F: Q.59, E.62 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.62 MG.17: 4 residues within 4Å: Chain G: D.132 Chain I: D.132 Chain N: D.132, E.135 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain G: E.135 Chain I: E.135 Chain N: E.135 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain G: Q.59, E.62 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain H: Q.59, E.62 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.62, H2O.31 MG.23: 3 residues within 4Å: Chain I: Q.59, E.62, E.63 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.62, H2O.36 MG.25: 3 residues within 4Å: Chain J: E.135 Chain L: E.135 Chain W: E.135 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain J: Q.59, E.62 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.62 MG.28: 2 residues within 4Å: Chain K: Q.59, E.62 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.62 MG.30: 2 residues within 4Å: Chain L: Q.59, E.62 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.62 MG.32: 4 residues within 4Å: Chain B: D.132, E.135 Chain M: D.132 Chain O: D.132 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain B: E.135 Chain M: E.135 Chain O: E.135 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain M: Q.59, E.62 No protein-ligand interaction detected (PLIP) MG.36: 2 residues within 4Å: Chain N: Q.59, E.62 2 PLIP interactions: 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.62, H2O.57 MG.38: 3 residues within 4Å: Chain O: Q.59, E.62, E.63 2 PLIP interactions: 1 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.62, H2O.62 MG.40: 3 residues within 4Å: Chain K: E.135 Chain P: E.135 Chain R: E.135 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain P: Q.59, E.62 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:E.62 MG.43: 2 residues within 4Å: Chain Q: Q.59, E.62 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.62 MG.45: 2 residues within 4Å: Chain R: Q.59, E.62 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:E.62 MG.47: 4 residues within 4Å: Chain H: D.132, E.135 Chain S: D.132 Chain U: D.132 No protein-ligand interaction detected (PLIP) MG.48: 3 residues within 4Å: Chain H: E.135 Chain S: E.135 Chain U: E.135 No protein-ligand interaction detected (PLIP) MG.49: 2 residues within 4Å: Chain S: Q.59, E.62 No protein-ligand interaction detected (PLIP) MG.51: 2 residues within 4Å: Chain T: Q.59, E.62 2 PLIP interactions: 1 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.62, H2O.82 MG.53: 3 residues within 4Å: Chain U: Q.59, E.62, E.63 2 PLIP interactions: 1 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.62, H2O.88 MG.55: 3 residues within 4Å: Chain E: E.135 Chain V: E.135 Chain X: E.135 No protein-ligand interaction detected (PLIP) MG.56: 2 residues within 4Å: Chain V: Q.59, E.62 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:E.62 MG.58: 2 residues within 4Å: Chain W: Q.59, E.62 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:E.62 MG.60: 2 residues within 4Å: Chain X: Q.59, E.62 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:E.62

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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