SMTL ID : 2z6m.2 (1 other biounit)

Crystal structure of Human Ferritin H8 as biotemplate for noble metal nanoparticle synthesis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-24-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.173 Chain D: H.173 Chain Q: H.173 Chain R: H.173 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:H.173 ZN.3: 11 residues within 4Å: Chain B: L.169, H.173 Chain H: L.169, H.173 Chain N: L.169, H.173 Chain T: L.169, H.173 Ligands: ZN.11, ZN.19, ZN.27 No protein-ligand interaction detected (PLIP) ZN.6: 7 residues within 4Å: Chain C: H.173 Chain I: H.173 Chain O: H.173 Chain U: H.173 Ligands: ZN.14, ZN.22, ZN.30 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain O, 1 interactions with chain C, 1 interactions with chain I Metal complexes: U:H.173, O:H.173, C:H.173, I:H.173 ZN.9: 4 residues within 4Å: Chain G: H.173 Chain J: H.173 Chain W: H.173 Chain X: H.173 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:H.173 ZN.11: 11 residues within 4Å: Chain B: L.169, H.173 Chain H: L.169, H.173 Chain N: L.169, H.173 Chain T: L.169, H.173 Ligands: ZN.3, ZN.19, ZN.27 No protein-ligand interaction detected (PLIP) ZN.14: 7 residues within 4Å: Chain C: H.173 Chain I: H.173 Chain O: H.173 Chain U: H.173 Ligands: ZN.6, ZN.22, ZN.30 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain O, 1 interactions with chain C, 1 interactions with chain I Metal complexes: U:H.173, O:H.173, C:H.173, I:H.173 ZN.17: 4 residues within 4Å: Chain K: H.173 Chain L: H.173 Chain M: H.173 Chain P: H.173 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:H.173 ZN.19: 11 residues within 4Å: Chain B: L.169, H.173 Chain H: L.169, H.173 Chain N: L.169, H.173 Chain T: L.169, H.173 Ligands: ZN.3, ZN.11, ZN.27 No protein-ligand interaction detected (PLIP) ZN.22: 7 residues within 4Å: Chain C: H.173 Chain I: H.173 Chain O: H.173 Chain U: H.173 Ligands: ZN.6, ZN.14, ZN.30 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain O, 1 interactions with chain I, 1 interactions with chain C Metal complexes: U:H.173, O:H.173, I:H.173, C:H.173 ZN.25: 4 residues within 4Å: Chain E: H.173 Chain F: H.173 Chain S: H.173 Chain V: H.173 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.173 ZN.27: 11 residues within 4Å: Chain B: L.169, H.173 Chain H: L.169, H.173 Chain N: L.169, H.173 Chain T: L.169, H.173 Ligands: ZN.3, ZN.11, ZN.19 No protein-ligand interaction detected (PLIP) ZN.30: 7 residues within 4Å: Chain C: H.173 Chain I: H.173 Chain O: H.173 Chain U: H.173 Ligands: ZN.6, ZN.14, ZN.22 4 PLIP interactions: 1 interactions with chain U, 1 interactions with chain O, 1 interactions with chain I, 1 interactions with chain C Metal complexes: U:H.173, O:H.173, I:H.173, C:H.173

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.131, E.134 Chain C: D.131, E.134 Chain E: D.131, E.134 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C, 1 interactions with chain A Metal complexes: E:D.131, E:E.134, C:D.131, C:E.134, A:D.131 CA.4: 6 residues within 4Å: Chain B: D.131, E.134 Chain D: D.131, E.134 Chain F: D.131, E.134 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D, 1 interactions with chain B Metal complexes: F:D.131, F:E.134, D:D.131, D:E.134, B:E.134 CA.10: 6 residues within 4Å: Chain G: D.131, E.134 Chain I: D.131, E.134 Chain K: D.131, E.134 5 PLIP interactions: 2 interactions with chain K, 2 interactions with chain I, 1 interactions with chain G Metal complexes: K:D.131, K:E.134, I:D.131, I:E.134, G:D.131 CA.12: 6 residues within 4Å: Chain H: D.131, E.134 Chain J: D.131, E.134 Chain L: D.131, E.134 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain H, 2 interactions with chain L Metal complexes: J:D.131, J:E.134, H:E.134, L:D.131, L:E.134 CA.18: 6 residues within 4Å: Chain M: D.131, E.134 Chain O: D.131, E.134 Chain Q: D.131, E.134 5 PLIP interactions: 1 interactions with chain M, 2 interactions with chain Q, 2 interactions with chain O Metal complexes: M:D.131, Q:D.131, Q:E.134, O:D.131, O:E.134 CA.20: 6 residues within 4Å: Chain N: D.131, E.134 Chain P: D.131, E.134 Chain R: D.131, E.134 5 PLIP interactions: 1 interactions with chain N, 2 interactions with chain R, 2 interactions with chain P Metal complexes: N:E.134, R:D.131, R:E.134, P:D.131, P:E.134 CA.26: 6 residues within 4Å: Chain S: D.131, E.134 Chain U: D.131, E.134 Chain W: D.131, E.134 5 PLIP interactions: 1 interactions with chain S, 2 interactions with chain W, 2 interactions with chain U Metal complexes: S:D.131, W:D.131, W:E.134, U:D.131, U:E.134 CA.28: 6 residues within 4Å: Chain T: D.131, E.134 Chain V: D.131, E.134 Chain X: D.131, E.134 5 PLIP interactions: 2 interactions with chain V, 2 interactions with chain X, 1 interactions with chain T Metal complexes: V:D.131, V:E.134, X:D.131, X:E.134, T:E.134

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

MPD.5: 8 residues within 4Å: Chain B: L.28, S.31, Y.32, L.35, R.63 Chain V: L.28, S.31, Y.32 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain V Hydrophobic interactions: B:L.28, B:Y.32, B:L.35, B:R.63, V:Y.32 MPD.7: 10 residues within 4Å: Chain C: L.28, S.31, Y.32, R.63, I.85 Chain Q: L.28, S.31, Y.32, L.35, R.63 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain Q Hydrophobic interactions: C:Y.32, C:I.85, Q:L.28, Q:Y.32, Q:L.35 Hydrogen bonds: C:S.31, C:S.31, Q:S.31 Water bridges: Q:S.59 MPD.8: 6 residues within 4Å: Chain A: S.31, Y.32, R.63 Chain F: S.31, Y.32, R.63 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain F Hydrophobic interactions: A:Y.32, F:Y.32, F:R.63 Hydrogen bonds: A:S.31, A:S.31, F:S.31 Water bridges: F:S.59 MPD.13: 8 residues within 4Å: Chain H: L.28, S.31, Y.32, L.35, R.63 Chain P: L.28, S.31, Y.32 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain P Hydrophobic interactions: H:L.28, H:Y.32, H:L.35, H:R.63, P:Y.32 MPD.15: 10 residues within 4Å: Chain I: L.28, S.31, Y.32, R.63, I.85 Chain W: L.28, S.31, Y.32, L.35, R.63 9 PLIP interactions: 5 interactions with chain W, 4 interactions with chain I Hydrophobic interactions: W:L.28, W:Y.32, W:L.35, I:Y.32, I:I.85 Hydrogen bonds: W:S.31, I:S.31, I:S.31 Water bridges: W:S.59 MPD.16: 6 residues within 4Å: Chain G: S.31, Y.32, R.63 Chain L: S.31, Y.32, R.63 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain L Hydrophobic interactions: G:Y.32, L:Y.32, L:R.63 Hydrogen bonds: G:S.31, G:S.31, L:S.31 Water bridges: L:S.59 MPD.21: 8 residues within 4Å: Chain D: L.28, S.31, Y.32 Chain N: L.28, S.31, Y.32, L.35, R.63 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain D Hydrophobic interactions: N:L.28, N:Y.32, N:L.35, N:R.63, D:Y.32 MPD.23: 10 residues within 4Å: Chain K: L.28, S.31, Y.32, L.35, R.63 Chain O: L.28, S.31, Y.32, R.63, I.85 9 PLIP interactions: 5 interactions with chain K, 4 interactions with chain O Hydrophobic interactions: K:L.28, K:Y.32, K:L.35, O:Y.32, O:I.85 Hydrogen bonds: K:S.31, O:S.31, O:S.31 Water bridges: K:S.59 MPD.24: 6 residues within 4Å: Chain M: S.31, Y.32, R.63 Chain R: S.31, Y.32, R.63 7 PLIP interactions: 3 interactions with chain M, 4 interactions with chain R Hydrophobic interactions: M:Y.32, R:Y.32, R:R.63 Hydrogen bonds: M:S.31, M:S.31, R:S.31 Water bridges: R:S.59 MPD.29: 8 residues within 4Å: Chain J: L.28, S.31, Y.32 Chain T: L.28, S.31, Y.32, L.35, R.63 5 PLIP interactions: 4 interactions with chain T, 1 interactions with chain J Hydrophobic interactions: T:L.28, T:Y.32, T:L.35, T:R.63, J:Y.32 MPD.31: 10 residues within 4Å: Chain E: L.28, S.31, Y.32, L.35, R.63 Chain U: L.28, S.31, Y.32, R.63, I.85 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain U Hydrophobic interactions: E:L.28, E:Y.32, E:L.35, U:Y.32, U:I.85 Hydrogen bonds: E:S.31, U:S.31, U:S.31 Water bridges: E:S.59 MPD.32: 6 residues within 4Å: Chain S: S.31, Y.32, R.63 Chain X: S.31, Y.32, R.63 7 PLIP interactions: 4 interactions with chain X, 3 interactions with chain S Hydrophobic interactions: X:Y.32, X:R.63, S:Y.32 Hydrogen bonds: X:S.31, S:S.31, S:S.31 Water bridges: X:S.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Butts, C.A. et al., Directing noble metal ion chemistry within a designed ferritin protein. Biochemistry (2008)

Release Date

2008-07-22

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

Related Entries With Identical Sequence