SMTL ID : 6h6t.1 (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.7: 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.9: 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.11: 4 residues within 4Å: Chain E: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.28, E:E.63, E:H.66 FE.14: 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.16: 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.19: 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.22: 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.24: 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.26: 4 residues within 4Å: Chain K: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.28, K:E.63, K:H.66 FE.29: 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.31: 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.34: 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.37: 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.39: 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.41: 4 residues within 4Å: Chain Q: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.28, Q:E.63, Q:H.66 FE.44: 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.46: 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.49: 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.52: 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.54: 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.56: 4 residues within 4Å: Chain W: E.28, E.63, H.66, Q.142 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:E.28, W:E.63, W:H.66 FE.59: 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: R.26, D.85, I.86, Q.87 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.26 Hydrogen bonds: A:Q.87, A:Q.87 Salt bridges: A:R.26 ACT.17: 4 residues within 4Å: Chain G: R.26, D.85, I.86, Q.87 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:R.26 Hydrogen bonds: G:Q.87, G:Q.87 Salt bridges: G:R.26 ACT.32: 4 residues within 4Å: Chain M: R.26, D.85, I.86, Q.87 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:R.26 Hydrogen bonds: M:Q.87, M:Q.87 Salt bridges: M:R.26 ACT.47: 4 residues within 4Å: Chain S: R.26, D.85, I.86, Q.87 4 PLIP interactions: 4 interactions with chain S Hydrophobic interactions: S:R.26 Hydrogen bonds: S:Q.87, S:Q.87 Salt bridges: S:R.26

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.132, E.135 Chain D: D.132, E.135 Chain F: D.132, E.135 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain F Metal complexes: D:E.135, A:E.135, F:E.135 MG.5: 5 residues within 4Å: Chain B: D.132, E.135 Chain C: E.135 Chain E: D.132, E.135 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 1 interactions with chain C Metal complexes: B:E.135, E:E.135, C:E.135 MG.18: 6 residues within 4Å: Chain G: D.132, E.135 Chain J: D.132, E.135 Chain L: D.132, E.135 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain L, 1 interactions with chain G Metal complexes: J:E.135, L:E.135, G:E.135 MG.20: 5 residues within 4Å: Chain H: D.132, E.135 Chain I: E.135 Chain K: D.132, E.135 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain H, 1 interactions with chain K Metal complexes: I:E.135, H:E.135, K:E.135 MG.33: 6 residues within 4Å: Chain M: D.132, E.135 Chain P: D.132, E.135 Chain R: D.132, E.135 3 PLIP interactions: 1 interactions with chain R, 1 interactions with chain P, 1 interactions with chain M Metal complexes: R:E.135, P:E.135, M:E.135 MG.35: 5 residues within 4Å: Chain N: D.132, E.135 Chain O: E.135 Chain Q: D.132, E.135 3 PLIP interactions: 1 interactions with chain N, 1 interactions with chain O, 1 interactions with chain Q Metal complexes: N:E.135, O:E.135, Q:E.135 MG.48: 6 residues within 4Å: Chain S: D.132, E.135 Chain V: D.132, E.135 Chain X: D.132, E.135 3 PLIP interactions: 1 interactions with chain V, 1 interactions with chain S, 1 interactions with chain X Metal complexes: V:E.135, S:E.135, X:E.135 MG.50: 5 residues within 4Å: Chain T: D.132, E.135 Chain U: E.135 Chain W: D.132, E.135 3 PLIP interactions: 1 interactions with chain W, 1 interactions with chain T, 1 interactions with chain U Metal complexes: W:E.135, T:E.135, U:E.135

12 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain C: H.174 Chain D: H.174 Chain M: H.174 Chain N: H.174 Ligands: CL.8 4 PLIP interactions: 1 interactions with chain M, 1 interactions with chain D, 1 interactions with chain N, 1 interactions with chain C Metal complexes: M:H.174, D:H.174, N:H.174, C:H.174 ZN.10: 11 residues within 4Å: Chain E: H.174 Chain K: H.174 Chain Q: H.174 Chain W: H.174 Ligands: CL.12, ZN.25, CL.27, ZN.40, CL.42, ZN.55, CL.57 4 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain W, 1 interactions with chain K, 1 interactions with chain E Metal complexes: Q:H.174, W:H.174, K:H.174, E:H.174 ZN.13: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: CL.15, ZN.28, CL.30, ZN.43, CL.45, ZN.58, CL.60 4 PLIP interactions: 1 interactions with chain L, 1 interactions with chain R, 1 interactions with chain F, 1 interactions with chain X Metal complexes: L:H.174, R:H.174, F:H.174, X:H.174 ZN.21: 5 residues within 4Å: Chain I: H.174 Chain J: H.174 Chain S: H.174 Chain T: H.174 Ligands: CL.23 4 PLIP interactions: 1 interactions with chain T, 1 interactions with chain I, 1 interactions with chain S, 1 interactions with chain J Metal complexes: T:H.174, I:H.174, S:H.174, J:H.174 ZN.25: 11 residues within 4Å: Chain E: H.174 Chain K: H.174 Chain Q: H.174 Chain W: H.174 Ligands: ZN.10, CL.12, CL.27, ZN.40, CL.42, ZN.55, CL.57 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain K, 1 interactions with chain Q, 1 interactions with chain W Metal complexes: E:H.174, K:H.174, Q:H.174, W:H.174 ZN.28: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: ZN.13, CL.15, CL.30, ZN.43, CL.45, ZN.58, CL.60 4 PLIP interactions: 1 interactions with chain R, 1 interactions with chain L, 1 interactions with chain F, 1 interactions with chain X Metal complexes: R:H.174, L:H.174, F:H.174, X:H.174 ZN.36: 5 residues within 4Å: Chain G: H.174 Chain H: H.174 Chain O: H.174 Chain P: H.174 Ligands: CL.38 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain O, 1 interactions with chain H, 1 interactions with chain P Metal complexes: G:H.174, O:H.174, H:H.174, P:H.174 ZN.40: 11 residues within 4Å: Chain E: H.174 Chain K: H.174 Chain Q: H.174 Chain W: H.174 Ligands: ZN.10, CL.12, ZN.25, CL.27, CL.42, ZN.55, CL.57 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain W, 1 interactions with chain E, 1 interactions with chain Q Metal complexes: K:H.174, W:H.174, E:H.174, Q:H.174 ZN.43: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: ZN.13, CL.15, ZN.28, CL.30, CL.45, ZN.58, CL.60 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain X, 1 interactions with chain R, 1 interactions with chain L Metal complexes: F:H.174, X:H.174, R:H.174, L:H.174 ZN.51: 5 residues within 4Å: Chain A: H.174 Chain B: H.174 Chain U: H.174 Chain V: H.174 Ligands: CL.53 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain V, 1 interactions with chain B, 1 interactions with chain U Metal complexes: A:H.174, V:H.174, B:H.174, U:H.174 ZN.55: 11 residues within 4Å: Chain E: H.174 Chain K: H.174 Chain Q: H.174 Chain W: H.174 Ligands: ZN.10, CL.12, ZN.25, CL.27, ZN.40, CL.42, CL.57 4 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain W, 1 interactions with chain E, 1 interactions with chain K Metal complexes: Q:H.174, W:H.174, E:H.174, K:H.174 ZN.58: 11 residues within 4Å: Chain F: H.174 Chain L: H.174 Chain R: H.174 Chain X: H.174 Ligands: ZN.13, CL.15, ZN.28, CL.30, ZN.43, CL.45, CL.60 4 PLIP interactions: 1 interactions with chain X, 1 interactions with chain R, 1 interactions with chain F, 1 interactions with chain L Metal complexes: X:H.174, R:H.174, F:H.174, L:H.174

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

CL.8: 6 residues within 4Å: Chain C: H.174 Chain D: H.174 Chain M: L.170, H.174 Chain N: H.174 Ligands: ZN.6 Ligand excluded by PLIP CL.12: 15 residues within 4Å: Chain E: L.170, H.174 Chain K: L.170, H.174 Chain Q: L.170, H.174 Chain W: L.170, H.174 Ligands: ZN.10, ZN.25, CL.27, ZN.40, CL.42, ZN.55, CL.57 Ligand excluded by PLIP CL.15: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: ZN.13, ZN.28, CL.30, ZN.43, CL.45, ZN.58, CL.60 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain I: H.174 Chain J: H.174 Chain S: L.170, H.174 Chain T: H.174 Ligands: ZN.21 Ligand excluded by PLIP CL.27: 15 residues within 4Å: Chain E: L.170, H.174 Chain K: L.170, H.174 Chain Q: L.170, H.174 Chain W: L.170, H.174 Ligands: ZN.10, CL.12, ZN.25, ZN.40, CL.42, ZN.55, CL.57 Ligand excluded by PLIP CL.30: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: ZN.13, CL.15, ZN.28, ZN.43, CL.45, ZN.58, CL.60 Ligand excluded by PLIP CL.38: 6 residues within 4Å: Chain G: L.170, H.174 Chain H: H.174 Chain O: H.174 Chain P: H.174 Ligands: ZN.36 Ligand excluded by PLIP CL.42: 15 residues within 4Å: Chain E: L.170, H.174 Chain K: L.170, H.174 Chain Q: L.170, H.174 Chain W: L.170, H.174 Ligands: ZN.10, CL.12, ZN.25, CL.27, ZN.40, ZN.55, CL.57 Ligand excluded by PLIP CL.45: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: ZN.13, CL.15, ZN.28, CL.30, ZN.43, ZN.58, CL.60 Ligand excluded by PLIP CL.53: 6 residues within 4Å: Chain A: L.170, H.174 Chain B: H.174 Chain U: H.174 Chain V: H.174 Ligands: ZN.51 Ligand excluded by PLIP CL.57: 15 residues within 4Å: Chain E: L.170, H.174 Chain K: L.170, H.174 Chain Q: L.170, H.174 Chain W: L.170, H.174 Ligands: ZN.10, CL.12, ZN.25, CL.27, ZN.40, CL.42, ZN.55 Ligand excluded by PLIP CL.60: 15 residues within 4Å: Chain F: L.170, H.174 Chain L: L.170, H.174 Chain R: L.170, H.174 Chain X: L.170, H.174 Ligands: ZN.13, CL.15, ZN.28, CL.30, ZN.43, CL.45, ZN.58 Ligand excluded by PLIP

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
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

Related Entries With Identical Sequence