SMTL ID : 2z6m.1 (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

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.173 Chain D: H.173 Chain M: H.173 Chain P: H.173 Ligands: ZN.17 No protein-ligand interaction detected (PLIP) ZN.3: 5 residues within 4Å: Chain B: L.169, H.173 Chain K: H.173 Chain L: H.173 Chain O: H.173 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.173 ZN.9: 5 residues within 4Å: Chain G: H.173 Chain J: H.173 Chain S: H.173 Chain V: H.173 Ligands: ZN.25 No protein-ligand interaction detected (PLIP) ZN.11: 5 residues within 4Å: Chain E: H.173 Chain F: H.173 Chain H: L.169, H.173 Chain U: H.173 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.173 ZN.17: 5 residues within 4Å: Chain A: H.173 Chain D: H.173 Chain M: H.173 Chain P: H.173 Ligands: ZN.1 No protein-ligand interaction detected (PLIP) ZN.19: 5 residues within 4Å: Chain C: H.173 Chain N: L.169, H.173 Chain W: H.173 Chain X: H.173 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:H.173 ZN.25: 5 residues within 4Å: Chain G: H.173 Chain J: H.173 Chain S: H.173 Chain V: H.173 Ligands: ZN.9 No protein-ligand interaction detected (PLIP) ZN.27: 5 residues within 4Å: Chain I: H.173 Chain Q: H.173 Chain R: H.173 Chain T: L.169, H.173 1 PLIP interactions: 1 interactions with chain T Metal complexes: T: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: 1 interactions with chain E, 2 interactions with chain C, 2 interactions with chain A Metal complexes: E:E.134, C:D.131, C:E.134, A:D.131, A:E.134 CA.4: 6 residues within 4Å: Chain B: D.131, E.134 Chain D: D.131, E.134 Chain F: D.131, E.134 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D Metal complexes: F:D.131, F:E.134, D:D.131, D: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 G, 2 interactions with chain I, 1 interactions with chain K Metal complexes: G:D.131, G:E.134, I:D.131, I:E.134, K:E.134 CA.12: 6 residues within 4Å: Chain H: D.131, E.134 Chain J: D.131, E.134 Chain L: D.131, E.134 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain J Metal complexes: L:D.131, L:E.134, J:D.131, J: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: 2 interactions with chain M, 2 interactions with chain O, 1 interactions with chain Q Metal complexes: M:D.131, M:E.134, O:D.131, O:E.134, Q: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 4 PLIP interactions: 2 interactions with chain R, 2 interactions with chain P Metal complexes: 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: 2 interactions with chain U, 2 interactions with chain S, 1 interactions with chain W Metal complexes: U:D.131, U:E.134, S:D.131, S:E.134, W: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 4 PLIP interactions: 2 interactions with chain V, 2 interactions with chain X Metal complexes: V:D.131, V:E.134, X:D.131, X:E.134

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

MPD.5: 9 residues within 4Å: Chain B: L.28, S.31, Y.32 Chain H: L.28, S.31, Y.32, L.35, R.63 Ligands: MPD.13 Ligand excluded by PLIP MPD.6: 9 residues within 4Å: Chain C: S.31, Y.32, R.63, I.85 Chain P: L.28, S.31, Y.32, R.63, I.85 Ligand excluded by PLIP MPD.7: 9 residues within 4Å: Chain E: L.28, S.31, Y.32, L.35, R.63 Chain W: L.28, S.31, Y.32 Ligands: MPD.31 Ligand excluded by PLIP MPD.8: 7 residues within 4Å: Chain A: L.28, S.31, Y.32 Chain F: L.28, S.31, Y.32, L.35 Ligand excluded by PLIP MPD.13: 9 residues within 4Å: Chain B: L.28, S.31, Y.32, L.35, R.63 Chain H: L.28, S.31, Y.32 Ligands: MPD.5 Ligand excluded by PLIP MPD.14: 9 residues within 4Å: Chain I: S.31, Y.32, R.63, I.85 Chain V: L.28, S.31, Y.32, R.63, I.85 Ligand excluded by PLIP MPD.15: 9 residues within 4Å: Chain K: L.28, S.31, Y.32, L.35, R.63 Chain Q: L.28, S.31, Y.32 Ligands: MPD.23 Ligand excluded by PLIP MPD.16: 7 residues within 4Å: Chain G: L.28, S.31, Y.32 Chain L: L.28, S.31, Y.32, L.35 Ligand excluded by PLIP MPD.21: 9 residues within 4Å: Chain N: L.28, S.31, Y.32 Chain T: L.28, S.31, Y.32, L.35, R.63 Ligands: MPD.29 Ligand excluded by PLIP MPD.22: 9 residues within 4Å: Chain D: L.28, S.31, Y.32, R.63, I.85 Chain O: S.31, Y.32, R.63, I.85 Ligand excluded by PLIP MPD.23: 9 residues within 4Å: Chain K: L.28, S.31, Y.32 Chain Q: L.28, S.31, Y.32, L.35, R.63 Ligands: MPD.15 Ligand excluded by PLIP MPD.24: 7 residues within 4Å: Chain M: L.28, S.31, Y.32 Chain R: L.28, S.31, Y.32, L.35 Ligand excluded by PLIP MPD.29: 9 residues within 4Å: Chain N: L.28, S.31, Y.32, L.35, R.63 Chain T: L.28, S.31, Y.32 Ligands: MPD.21 Ligand excluded by PLIP MPD.30: 9 residues within 4Å: Chain J: L.28, S.31, Y.32, R.63, I.85 Chain U: S.31, Y.32, R.63, I.85 Ligand excluded by PLIP MPD.31: 9 residues within 4Å: Chain E: L.28, S.31, Y.32 Chain W: L.28, S.31, Y.32, L.35, R.63 Ligands: MPD.7 Ligand excluded by PLIP MPD.32: 7 residues within 4Å: Chain S: L.28, S.31, Y.32 Chain X: L.28, S.31, Y.32, L.35 Ligand excluded by PLIP

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
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