SMTL ID : 6h6t.2 (1 other biounit)

Binary crystal structure of positively and negatively supercharged variants Ftn(pos) and Ftn(neg) from human heavy chain ferritin (propandiol condition, coordination number 8)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.28, A:E.63, A:H.66 FE.4: 4 residues within 4Å: Chain B: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.28, B:E.63, B:H.66 FE.5: 4 residues within 4Å: Chain C: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.28, C:E.63, C:H.66 FE.7: 4 residues within 4Å: Chain D: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.28, D:E.63, D:H.66 FE.10: 4 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.28, E:E.63 FE.12: 4 residues within 4Å: Chain F: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.28, F:E.63, F:H.66 FE.14: 4 residues within 4Å: Chain G: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.28, G:E.63, G:H.66 FE.17: 4 residues within 4Å: Chain H: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.28, H:E.63, H:H.66 FE.18: 4 residues within 4Å: Chain I: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.28, I:E.63, I:H.66 FE.20: 4 residues within 4Å: Chain J: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.28, J:E.63, J:H.66 FE.23: 4 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.28, K:E.63 FE.25: 4 residues within 4Å: Chain L: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.28, L:E.63, L:H.66 FE.27: 4 residues within 4Å: Chain M: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:E.28, M:E.63, M:H.66 FE.30: 4 residues within 4Å: Chain N: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:E.28, N:E.63, N:H.66 FE.31: 4 residues within 4Å: Chain O: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:E.28, O:E.63, O:H.66 FE.33: 4 residues within 4Å: Chain P: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.28, P:E.63, P:H.66 FE.36: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, Q.142 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:E.28, Q:E.63 FE.38: 4 residues within 4Å: Chain R: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.28, R:E.63, R:H.66 FE.40: 4 residues within 4Å: Chain S: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.28, S:E.63, S:H.66 FE.43: 4 residues within 4Å: Chain T: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.28, T:E.63, T:H.66 FE.44: 4 residues within 4Å: Chain U: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.28, U:E.63, U:H.66 FE.46: 4 residues within 4Å: Chain V: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:E.28, V:E.63, V:H.66 FE.49: 4 residues within 4Å: Chain W: E.28, E.63, H.66, Q.142 2 PLIP interactions: 2 interactions with chain W Metal complexes: W:E.28, W:E.63 FE.51: 4 residues within 4Å: Chain X: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.28, X:E.63, X:H.66

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: Y.30, D.90, E.103, E.106 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.106 Hydrogen bonds: A:Y.30, A:E.103 ACT.15: 4 residues within 4Å: Chain G: Y.30, D.90, E.103, E.106 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:E.106 Hydrogen bonds: G:Y.30, G:E.103 ACT.28: 4 residues within 4Å: Chain M: Y.30, D.90, E.103, E.106 3 PLIP interactions: 3 interactions with chain M Hydrophobic interactions: M:E.106 Hydrogen bonds: M:Y.30, M:E.103 ACT.41: 4 residues within 4Å: Chain S: Y.30, D.90, E.103, E.106 3 PLIP interactions: 3 interactions with chain S Hydrophobic interactions: S:E.106 Hydrogen bonds: S:Y.30, S:E.103

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

CL.3: 7 residues within 4Å: Chain A: L.170, H.174 Chain B: H.174 Chain E: L.170, H.174 Chain U: H.174 Ligands: ZN.9 Ligand excluded by PLIP CL.8: 15 residues within 4Å: Chain D: L.170, H.174 Chain J: L.170, H.174 Chain P: L.170, H.174 Chain V: L.170, H.174 Ligands: ZN.6, ZN.19, CL.21, ZN.32, CL.34, ZN.45, CL.47 Ligand excluded by PLIP CL.13: 13 residues within 4Å: Chain F: H.174 Chain L: L.170, H.174 Chain R: H.174 Chain X: L.170, H.174 Ligands: ZN.11, ZN.24, CL.26, ZN.37, CL.39, ZN.50, CL.52 Ligand excluded by PLIP CL.16: 7 residues within 4Å: Chain G: L.170, H.174 Chain H: H.174 Chain K: L.170, H.174 Chain O: H.174 Ligands: ZN.22 Ligand excluded by PLIP CL.21: 15 residues within 4Å: Chain D: L.170, H.174 Chain J: L.170, H.174 Chain P: L.170, H.174 Chain V: L.170, H.174 Ligands: ZN.6, CL.8, ZN.19, ZN.32, CL.34, ZN.45, CL.47 Ligand excluded by PLIP CL.26: 13 residues within 4Å: Chain F: L.170, H.174 Chain L: H.174 Chain R: L.170, H.174 Chain X: H.174 Ligands: ZN.11, CL.13, ZN.24, ZN.37, CL.39, ZN.50, CL.52 Ligand excluded by PLIP CL.29: 7 residues within 4Å: Chain C: H.174 Chain M: L.170, H.174 Chain N: H.174 Chain Q: L.170, H.174 Ligands: ZN.35 Ligand excluded by PLIP CL.34: 15 residues within 4Å: Chain D: L.170, H.174 Chain J: L.170, H.174 Chain P: L.170, H.174 Chain V: L.170, H.174 Ligands: ZN.6, CL.8, ZN.19, CL.21, ZN.32, ZN.45, CL.47 Ligand excluded by PLIP CL.39: 13 residues within 4Å: Chain F: L.170, H.174 Chain L: H.174 Chain R: H.174 Chain X: L.170, H.174 Ligands: ZN.11, CL.13, ZN.24, CL.26, ZN.37, ZN.50, CL.52 Ligand excluded by PLIP CL.42: 7 residues within 4Å: Chain I: H.174 Chain S: L.170, H.174 Chain T: H.174 Chain W: L.170, H.174 Ligands: ZN.48 Ligand excluded by PLIP CL.47: 15 residues within 4Å: Chain D: L.170, H.174 Chain J: L.170, H.174 Chain P: L.170, H.174 Chain V: L.170, H.174 Ligands: ZN.6, CL.8, ZN.19, CL.21, ZN.32, CL.34, ZN.45 Ligand excluded by PLIP CL.52: 13 residues within 4Å: Chain F: H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: H.174 Ligands: ZN.11, CL.13, ZN.24, CL.26, ZN.37, CL.39, ZN.50 Ligand excluded by PLIP

12 x ZN: ZINC ION(Non-covalent)

ZN.6: 11 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain P: H.174 Chain V: H.174 Ligands: CL.8, ZN.19, CL.21, ZN.32, CL.34, ZN.45, CL.47 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain P, 1 interactions with chain V, 1 interactions with chain J Metal complexes: D:H.174, P:H.174, V:H.174, J:H.174 ZN.9: 5 residues within 4Å: Chain A: H.174 Chain B: H.174 Chain E: H.174 Chain U: H.174 Ligands: CL.3 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain U, 1 interactions with chain B, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:H.174, U:H.174, B:H.174, E:H.174, H2O.10 ZN.11: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: CL.13, ZN.24, CL.26, ZN.37, CL.39, ZN.50, CL.52 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain L, 1 interactions with chain X, 1 interactions with chain R Metal complexes: F:H.174, L:H.174, X:H.174, R:H.174 ZN.19: 11 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain P: H.174 Chain V: H.174 Ligands: ZN.6, CL.8, CL.21, ZN.32, CL.34, ZN.45, CL.47 4 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 1 interactions with chain V, 1 interactions with chain P Metal complexes: J:H.174, D:H.174, V:H.174, P:H.174 ZN.22: 5 residues within 4Å: Chain G: H.174 Chain H: H.174 Chain K: H.174 Chain O: H.174 Ligands: CL.16 5 PLIP interactions: 1 interactions with chain O, 1 interactions with chain K, 1 interactions with chain H, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: O:H.174, K:H.174, H:H.174, G:H.174, H2O.21 ZN.24: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: ZN.11, CL.13, CL.26, ZN.37, CL.39, ZN.50, CL.52 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain F, 1 interactions with chain R, 1 interactions with chain L Metal complexes: X:H.174, F:H.174, R:H.174, L:H.174 ZN.32: 11 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain P: H.174 Chain V: H.174 Ligands: ZN.6, CL.8, ZN.19, CL.21, CL.34, ZN.45, CL.47 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain V, 1 interactions with chain J, 1 interactions with chain P Metal complexes: D:H.174, V:H.174, J:H.174, P:H.174 ZN.35: 5 residues within 4Å: Chain C: H.174 Chain M: H.174 Chain N: H.174 Chain Q: H.174 Ligands: CL.29 5 PLIP interactions: 1 interactions with chain M, 1 interactions with chain Q, 1 interactions with chain C, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: M:H.174, Q:H.174, C:H.174, N:H.174, H2O.32 ZN.37: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: ZN.11, CL.13, ZN.24, CL.26, CL.39, ZN.50, CL.52 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain L, 1 interactions with chain X, 1 interactions with chain F Metal complexes: R:H.174, L:H.174, X:H.174, F:H.174 ZN.45: 11 residues within 4Å: Chain D: H.174 Chain J: H.174 Chain P: H.174 Chain V: H.174 Ligands: ZN.6, CL.8, ZN.19, CL.21, ZN.32, CL.34, CL.47 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain V, 1 interactions with chain J, 1 interactions with chain P Metal complexes: D:H.174, V:H.174, J:H.174, P:H.174 ZN.48: 5 residues within 4Å: Chain I: H.174 Chain S: H.174 Chain T: H.174 Chain W: H.174 Ligands: CL.42 5 PLIP interactions: 1 interactions with chain T, 1 interactions with chain S, 1 interactions with chain I, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: T:H.174, S:H.174, I:H.174, W:H.174, H2O.43 ZN.50: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: ZN.11, CL.13, ZN.24, CL.26, ZN.37, CL.39, CL.52 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain R, 1 interactions with chain X Metal complexes: L:H.174, F:H.174, R:H.174, X:H.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuenzle, M. et al., Self-assembly of protein crystals into different crystal structures using charged patches on oppositely charged ferritin protein containers. To Be Published

Release Date

2019-08-14

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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