SMTL ID : 1s3q.1

Crystal structures of a novel open pore ferritin from the hyperthermophilic Archaeon Archaeoglobus fulgidus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-24-mer

Ligands

48 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.19, E.52, H.55 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.19, A:E.52, A:H.55, H2O.35, H2O.69 ZN.2: 6 residues within 4Å: Chain A: Q.48, E.52, H.55, E.96, E.132 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.52, A:E.96, A:E.96, A:E.132, H2O.35 ZN.3: 4 residues within 4Å: Chain B: E.19, E.52, H.55 Ligands: ZN.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.19, B:E.52, B:H.55, H2O.96, H2O.146 ZN.4: 6 residues within 4Å: Chain B: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.52, B:E.96, B:E.96, B:E.132, H2O.96 ZN.5: 4 residues within 4Å: Chain C: E.19, E.52, H.55 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.19, C:E.52, C:H.55, H2O.191 ZN.6: 7 residues within 4Å: Chain C: Q.48, E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.52, C:E.96, C:E.96, C:E.132 ZN.7: 4 residues within 4Å: Chain D: E.19, E.52, H.55 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.19, D:E.52, D:H.55, H2O.228 ZN.8: 6 residues within 4Å: Chain D: Q.48, E.52, H.55, E.96, E.132 Ligands: ZN.7 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.52, D:E.96, D:E.96, D:E.132, H2O.228 ZN.9: 4 residues within 4Å: Chain E: E.19, E.52, H.55 Ligands: ZN.10 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.19, E:E.52, E:H.55 ZN.10: 6 residues within 4Å: Chain E: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.52, E:E.96, E:E.96, E:E.132, H2O.297 ZN.11: 4 residues within 4Å: Chain F: E.19, E.52, H.55 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.19, F:E.52, F:H.55 ZN.12: 6 residues within 4Å: Chain F: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.52, F:E.96, F:E.96, F:E.132, H2O.392 ZN.13: 4 residues within 4Å: Chain G: E.19, E.52, H.55 Ligands: ZN.14 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.19, G:E.52, G:H.55, H2O.477, H2O.491 ZN.14: 6 residues within 4Å: Chain G: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.52, G:E.96, G:E.96, G:E.132, H2O.477 ZN.15: 4 residues within 4Å: Chain H: E.19, E.52, H.55 Ligands: ZN.16 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.19, H:E.52, H:H.55 ZN.16: 6 residues within 4Å: Chain H: Q.48, E.52, E.96, Q.129, E.132 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.52, H:E.96, H:E.96, H:E.132, H2O.534 ZN.17: 4 residues within 4Å: Chain I: E.19, E.52, H.55 Ligands: ZN.18 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.19, I:E.52, I:H.55, H2O.593 ZN.18: 7 residues within 4Å: Chain I: Q.48, E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.17 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.52, I:E.96, I:E.96, I:E.132 ZN.19: 4 residues within 4Å: Chain J: E.19, E.52, H.55 Ligands: ZN.20 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.19, J:E.52, J:H.55, H2O.689 ZN.20: 4 residues within 4Å: Chain J: E.52, E.96, E.132 Ligands: ZN.19 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.52, J:E.96, J:E.96, J:E.132, H2O.660 ZN.21: 4 residues within 4Å: Chain K: E.19, E.52, H.55 Ligands: ZN.22 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.19, K:E.52, K:H.55, H2O.769 ZN.22: 6 residues within 4Å: Chain K: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.21 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.52, K:E.96, K:E.96, K:E.132, H2O.769 ZN.23: 4 residues within 4Å: Chain L: E.19, E.52, H.55 Ligands: ZN.24 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.19, L:E.52, L:H.55, H2O.834 ZN.24: 6 residues within 4Å: Chain L: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.23 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:E.52, L:E.96, L:E.96, L:E.132, H2O.834 ZN.25: 4 residues within 4Å: Chain M: E.19, E.52, H.55 Ligands: ZN.26 5 PLIP interactions: 3 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:E.19, M:E.52, M:H.55, H2O.901, H2O.935 ZN.26: 6 residues within 4Å: Chain M: Q.48, E.52, H.55, E.96, E.132 Ligands: ZN.25 5 PLIP interactions: 4 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.52, M:E.96, M:E.96, M:E.132, H2O.901 ZN.27: 4 residues within 4Å: Chain N: E.19, E.52, H.55 Ligands: ZN.28 5 PLIP interactions: 3 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:E.19, N:E.52, N:H.55, H2O.962, H2O.1012 ZN.28: 6 residues within 4Å: Chain N: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.27 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.52, N:E.96, N:E.96, N:E.132, H2O.962 ZN.29: 4 residues within 4Å: Chain O: E.19, E.52, H.55 Ligands: ZN.30 4 PLIP interactions: 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: O:E.19, O:E.52, O:H.55, H2O.1057 ZN.30: 7 residues within 4Å: Chain O: Q.48, E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.29 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:E.52, O:E.96, O:E.96, O:E.132 ZN.31: 4 residues within 4Å: Chain P: E.19, E.52, H.55 Ligands: ZN.32 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.19, P:E.52, P:H.55, H2O.1094 ZN.32: 6 residues within 4Å: Chain P: Q.48, E.52, H.55, E.96, E.132 Ligands: ZN.31 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.52, P:E.96, P:E.96, P:E.132, H2O.1094 ZN.33: 4 residues within 4Å: Chain Q: E.19, E.52, H.55 Ligands: ZN.34 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:E.19, Q:E.52, Q:H.55 ZN.34: 6 residues within 4Å: Chain Q: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.33 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.52, Q:E.96, Q:E.96, Q:E.132, H2O.1163 ZN.35: 4 residues within 4Å: Chain R: E.19, E.52, H.55 Ligands: ZN.36 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:E.19, R:E.52, R:H.55 ZN.36: 6 residues within 4Å: Chain R: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.35 5 PLIP interactions: 4 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:E.52, R:E.96, R:E.96, R:E.132, H2O.1258 ZN.37: 4 residues within 4Å: Chain S: E.19, E.52, H.55 Ligands: ZN.38 5 PLIP interactions: 3 interactions with chain S, 2 Ligand-Water interactions Metal complexes: S:E.19, S:E.52, S:H.55, H2O.1343, H2O.1357 ZN.38: 6 residues within 4Å: Chain S: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.37 5 PLIP interactions: 4 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.52, S:E.96, S:E.96, S:E.132, H2O.1343 ZN.39: 4 residues within 4Å: Chain T: E.19, E.52, H.55 Ligands: ZN.40 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:E.19, T:E.52, T:H.55 ZN.40: 6 residues within 4Å: Chain T: Q.48, E.52, E.96, Q.129, E.132 Ligands: ZN.39 5 PLIP interactions: 4 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.52, T:E.96, T:E.96, T:E.132, H2O.1400 ZN.41: 4 residues within 4Å: Chain U: E.19, E.52, H.55 Ligands: ZN.42 4 PLIP interactions: 3 interactions with chain U, 1 Ligand-Water interactions Metal complexes: U:E.19, U:E.52, U:H.55, H2O.1459 ZN.42: 7 residues within 4Å: Chain U: Q.48, E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.41 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:E.52, U:E.96, U:E.96, U:E.132 ZN.43: 4 residues within 4Å: Chain V: E.19, E.52, H.55 Ligands: ZN.44 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.19, V:E.52, V:H.55, H2O.1555 ZN.44: 4 residues within 4Å: Chain V: E.52, E.96, E.132 Ligands: ZN.43 5 PLIP interactions: 4 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.52, V:E.96, V:E.96, V:E.132, H2O.1526 ZN.45: 4 residues within 4Å: Chain W: E.19, E.52, H.55 Ligands: ZN.46 4 PLIP interactions: 3 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.19, W:E.52, W:H.55, H2O.1635 ZN.46: 6 residues within 4Å: Chain W: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.45 5 PLIP interactions: 4 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.52, W:E.96, W:E.96, W:E.132, H2O.1635 ZN.47: 4 residues within 4Å: Chain X: E.19, E.52, H.55 Ligands: ZN.48 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.19, X:E.52, X:H.55, H2O.1700 ZN.48: 6 residues within 4Å: Chain X: E.52, H.55, E.96, Q.129, E.132 Ligands: ZN.47 5 PLIP interactions: 4 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:E.52, X:E.96, X:E.96, X:E.132, H2O.1700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, E. et al., Crystal structures of a tetrahedral open pore ferritin from the hyperthermophilic archaeon Archaeoglobus fulgidus. Structure (2005)

Release Date

2005-04-12

Peptides

ferritin: 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

Related Entries With Identical Sequence