SMTL ID : 7k26.1

Crystal structure of Human H-chain Ferritin variant infused with Sodium Acrylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-24-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: E.27, E.62, H.65, Q.141 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.27, A:E.62, A:E.62, A:H.65 FE.4: 4 residues within 4Å: Chain B: E.27, E.62, H.65, Q.141 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.27, B:E.62, B:E.62, B:H.65 FE.8: 4 residues within 4Å: Chain C: E.27, E.62, H.65, Q.141 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.27, C:E.62 FE.10: 5 residues within 4Å: Chain D: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.27, D:E.62, D:E.62 FE.12: 4 residues within 4Å: Chain E: E.27, E.62, H.65, Q.141 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.27, E:E.62, E:H.65 FE.14: 5 residues within 4Å: Chain F: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.27, F:E.62, F:H.65 FE.16: 5 residues within 4Å: Chain G: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.27, G:E.62, G:H.65 FE.18: 5 residues within 4Å: Chain H: E.27, E.62, H.65, E.107, Q.141 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.27, H:E.62, H:E.62, H:H.65 FE.20: 4 residues within 4Å: Chain I: E.27, E.62, H.65, Q.141 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.27, I:E.62, I:H.65 FE.21: 4 residues within 4Å: Chain J: E.27, E.62, H.65, Q.141 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:E.62, J:E.62 FE.22: 4 residues within 4Å: Chain K: E.27, E.62, H.65, Q.141 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.27, K:E.62, K:E.62, K:H.65 FE.24: 5 residues within 4Å: Chain L: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.27, L:E.62, L:E.62 FE.27: 4 residues within 4Å: Chain M: E.27, E.62, H.65, Q.141 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:E.27, M:E.62, M:E.62, M:H.65 FE.30: 4 residues within 4Å: Chain N: E.27, E.62, H.65, Q.141 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:E.27, N:E.62, N:E.62, N:H.65 FE.34: 4 residues within 4Å: Chain O: E.27, E.62, H.65, Q.141 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:E.27, O:E.62 FE.36: 5 residues within 4Å: Chain P: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:E.27, P:E.62, P:E.62 FE.38: 4 residues within 4Å: Chain Q: E.27, E.62, H.65, Q.141 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.27, Q:E.62, Q:H.65 FE.40: 5 residues within 4Å: Chain R: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.27, R:E.62, R:H.65 FE.42: 5 residues within 4Å: Chain S: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:E.27, S:E.62, S:H.65 FE.44: 5 residues within 4Å: Chain T: E.27, E.62, H.65, E.107, Q.141 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:E.27, T:E.62, T:E.62, T:H.65 FE.46: 4 residues within 4Å: Chain U: E.27, E.62, H.65, Q.141 3 PLIP interactions: 3 interactions with chain U Metal complexes: U:E.27, U:E.62, U:H.65 FE.47: 4 residues within 4Å: Chain V: E.27, E.62, H.65, Q.141 2 PLIP interactions: 2 interactions with chain V Metal complexes: V:E.62, V:E.62 FE.48: 4 residues within 4Å: Chain W: E.27, E.62, H.65, Q.141 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:E.27, W:E.62, W:E.62, W:H.65 FE.50: 5 residues within 4Å: Chain X: E.27, E.62, H.65, V.110, Q.141 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:E.27, X:E.62, X:E.62

14 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: E.134 Chain C: E.134 Chain G: E.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.134 Water bridges: A:D.131 NA.3: 4 residues within 4Å: Chain A: H.173 Chain E: H.173 Chain F: H.173 Chain L: H.173 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.173 NA.5: 6 residues within 4Å: Chain B: D.131, E.134 Chain D: D.131, E.134 Chain F: D.131, E.134 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: B:D.131, F:D.131, D:E.134 NA.6: 6 residues within 4Å: Chain B: L.169, H.173 Chain H: L.169, H.173 Chain P: H.173 Chain S: H.173 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:H.173 NA.9: 6 residues within 4Å: Chain C: L.169, H.173 Chain J: H.173 Chain K: L.169, H.173 Chain U: H.173 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:H.173 NA.19: 7 residues within 4Å: Chain H: D.131, E.134 Chain L: D.131, E.134 Chain V: D.131, E.134 Ligands: NA.25 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain L Hydrogen bonds: V:D.131, V:E.134, L:D.131 NA.25: 4 residues within 4Å: Chain L: D.131 Chain V: D.131, T.135 Ligands: NA.19 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:T.135 NA.28: 3 residues within 4Å: Chain M: E.134 Chain O: E.134 Chain S: E.134 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain O Water bridges: M:E.134 Hydrogen bonds: O:E.134 NA.29: 4 residues within 4Å: Chain M: H.173 Chain Q: H.173 Chain R: H.173 Chain X: H.173 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:H.173 NA.31: 6 residues within 4Å: Chain N: D.131, E.134 Chain P: D.131, E.134 Chain R: D.131, E.134 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:D.131, P:E.134 NA.32: 6 residues within 4Å: Chain D: H.173 Chain G: H.173 Chain N: L.169, H.173 Chain T: L.169, H.173 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:H.173 NA.35: 6 residues within 4Å: Chain I: H.173 Chain O: L.169, H.173 Chain V: H.173 Chain W: L.169, H.173 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:H.173 NA.45: 7 residues within 4Å: Chain J: D.131, E.134 Chain T: D.131, E.134 Chain X: D.131, E.134 Ligands: NA.51 2 PLIP interactions: 1 interactions with chain T, 1 interactions with chain X Hydrogen bonds: T:D.131, X:E.134 NA.51: 4 residues within 4Å: Chain J: D.131, T.135 Chain X: D.131 Ligands: NA.45 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:D.131

14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 11 residues within 4Å: Chain B: L.28, S.31, Y.32, R.63 Chain N: L.28, S.31, Y.32, L.35, R.63, I.85 Ligands: MPD.33 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:L.28, N:S.31 MPD.11: 12 residues within 4Å: Chain A: L.28, S.31, Y.32, R.63, I.85 Chain D: L.28, S.31, Y.32, L.35, S.59, R.63, I.85 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.35, D:I.85 Hydrogen bonds: D:L.28, D:R.63 MPD.13: 10 residues within 4Å: Chain C: L.28, S.31, Y.32, L.35, R.63 Chain E: L.28, S.31, Y.32, R.63, I.85 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:Y.32, C:L.35 Hydrogen bonds: C:S.31, C:S.31, E:R.63 MPD.15: 12 residues within 4Å: Chain F: L.28, S.31, Y.32, L.35, R.63, I.85 Chain H: L.28, S.31, Y.32, S.59, R.63, I.85 9 PLIP interactions: 4 interactions with chain H, 5 interactions with chain F Hydrophobic interactions: H:L.28, H:Y.32, H:I.85, F:Y.32, F:L.35 Water bridges: H:R.63, F:S.59 Hydrogen bonds: F:S.31, F:R.63 MPD.17: 12 residues within 4Å: Chain G: L.28, S.31, Y.32, L.35, R.63, I.85 Chain J: L.28, S.31, Y.32, L.35, S.59, R.63 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.32 MPD.23: 12 residues within 4Å: Chain K: L.28, S.31, L.35, R.63, I.85 Chain W: L.28, S.31, Y.32, L.35, R.63, I.85 Ligands: MPD.49 4 PLIP interactions: 2 interactions with chain W, 2 interactions with chain K Hydrophobic interactions: W:Y.32, K:I.85 Hydrogen bonds: W:R.63, K:R.63 MPD.26: 13 residues within 4Å: Chain I: L.28, S.31, Y.32, S.59, R.63, I.85 Chain L: L.28, S.31, Y.32, L.35, S.59, R.63, I.85 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:I.85 Hydrogen bonds: L:S.31 MPD.33: 11 residues within 4Å: Chain B: L.28, S.31, Y.32, L.35, R.63, I.85 Chain N: L.28, S.31, Y.32, R.63 Ligands: MPD.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.28, B:S.31 MPD.37: 12 residues within 4Å: Chain M: L.28, S.31, Y.32, R.63, I.85 Chain P: L.28, S.31, Y.32, L.35, S.59, R.63, I.85 4 PLIP interactions: 4 interactions with chain P Hydrophobic interactions: P:L.35, P:I.85 Hydrogen bonds: P:L.28, P:R.63 MPD.39: 10 residues within 4Å: Chain O: L.28, S.31, Y.32, L.35, R.63 Chain Q: L.28, S.31, Y.32, R.63, I.85 5 PLIP interactions: 4 interactions with chain O, 1 interactions with chain Q Hydrophobic interactions: O:Y.32, O:L.35 Hydrogen bonds: O:S.31, O:S.31, Q:R.63 MPD.41: 12 residues within 4Å: Chain R: L.28, S.31, Y.32, L.35, R.63, I.85 Chain T: L.28, S.31, Y.32, S.59, R.63, I.85 9 PLIP interactions: 5 interactions with chain R, 4 interactions with chain T Hydrophobic interactions: R:Y.32, R:L.35, T:L.28, T:Y.32, T:I.85 Hydrogen bonds: R:S.31, R:R.63 Water bridges: R:S.59, T:R.63 MPD.43: 12 residues within 4Å: Chain S: L.28, S.31, Y.32, L.35, R.63, I.85 Chain V: L.28, S.31, Y.32, L.35, S.59, R.63 1 PLIP interactions: 1 interactions with chain S Hydrophobic interactions: S:Y.32 MPD.49: 12 residues within 4Å: Chain K: L.28, S.31, Y.32, L.35, R.63, I.85 Chain W: L.28, S.31, L.35, R.63, I.85 Ligands: MPD.23 4 PLIP interactions: 2 interactions with chain K, 2 interactions with chain W Hydrophobic interactions: K:Y.32, W:I.85 Hydrogen bonds: K:R.63, W:R.63 MPD.52: 13 residues within 4Å: Chain U: L.28, S.31, Y.32, S.59, R.63, I.85 Chain X: L.28, S.31, Y.32, L.35, S.59, R.63, I.85 2 PLIP interactions: 2 interactions with chain X Hydrophobic interactions: X:I.85 Hydrogen bonds: X:S.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, K. et al., Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks. J.Am.Chem.Soc. (2020)

Release Date

2020-11-11

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
G

H
H

I
I

J
J

K
K

L
L

M
A

N
B

O
C

P
D

Q
E

R
F

S
G

T
H

U
I

V
J

W
K

X
L

Ferritin heavy chain

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