SMTL ID : 5c6f.2 (1 other biounit)

Crystal structures of ferritin mutants reveal side-on binding to diiron and end-on cleavage of oxygen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-24-mer

Ligands

16 x FE: FE (III) ION(Non-functional Binders)(Non-covalent)

FE.1: 1 residues within 4Å: Ligands: FE.4 No protein-ligand interaction detected (PLIP) FE.4: 1 residues within 4Å: Ligands: FE.1 No protein-ligand interaction detected (PLIP) FE.6: 4 residues within 4Å: Chain D: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.56, D:E.100, D:E.136, H2O.29 FE.8: 4 residues within 4Å: Chain E: E.56, E.100, Q.133, E.136 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.56, E:E.56, E:E.100, E:E.136, H2O.37 FE.11: 1 residues within 4Å: Ligands: FE.14 No protein-ligand interaction detected (PLIP) FE.14: 1 residues within 4Å: Ligands: FE.11 No protein-ligand interaction detected (PLIP) FE.16: 4 residues within 4Å: Chain J: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:E.56, J:E.100, J:E.136, H2O.80 FE.18: 4 residues within 4Å: Chain K: E.56, E.100, Q.133, E.136 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.56, K:E.56, K:E.100, K:E.136, H2O.89 FE.21: 1 residues within 4Å: Ligands: FE.24 No protein-ligand interaction detected (PLIP) FE.24: 1 residues within 4Å: Ligands: FE.21 No protein-ligand interaction detected (PLIP) FE.26: 4 residues within 4Å: Chain P: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:E.56, P:E.100, P:E.136, H2O.132 FE.28: 4 residues within 4Å: Chain Q: E.56, E.100, Q.133, E.136 5 PLIP interactions: 4 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:E.56, Q:E.56, Q:E.100, Q:E.136, H2O.140 FE.31: 1 residues within 4Å: Ligands: FE.34 No protein-ligand interaction detected (PLIP) FE.34: 1 residues within 4Å: Ligands: FE.31 No protein-ligand interaction detected (PLIP) FE.36: 4 residues within 4Å: Chain V: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:E.56, V:E.100, V:E.136, H2O.184 FE.38: 4 residues within 4Å: Chain W: E.56, E.100, Q.133, E.136 5 PLIP interactions: 4 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:E.56, W:E.56, W:E.100, W:E.136, H2O.192

24 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 5 residues within 4Å: Chain A: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.3: 5 residues within 4Å: Chain B: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.5: 4 residues within 4Å: Chain C: H.59, K.62, Y.129, E.132 Ligand excluded by PLIP IMD.7: 5 residues within 4Å: Chain D: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.9: 5 residues within 4Å: Chain E: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.10: 5 residues within 4Å: Chain F: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.12: 5 residues within 4Å: Chain G: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.13: 5 residues within 4Å: Chain H: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.15: 4 residues within 4Å: Chain I: H.59, K.62, Y.129, E.132 Ligand excluded by PLIP IMD.17: 5 residues within 4Å: Chain J: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.19: 5 residues within 4Å: Chain K: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.20: 5 residues within 4Å: Chain L: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.22: 5 residues within 4Å: Chain M: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.23: 5 residues within 4Å: Chain N: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.25: 4 residues within 4Å: Chain O: H.59, K.62, Y.129, E.132 Ligand excluded by PLIP IMD.27: 5 residues within 4Å: Chain P: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.29: 5 residues within 4Å: Chain Q: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.30: 5 residues within 4Å: Chain R: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.32: 5 residues within 4Å: Chain S: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.33: 5 residues within 4Å: Chain T: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.35: 4 residues within 4Å: Chain U: H.59, K.62, Y.129, E.132 Ligand excluded by PLIP IMD.37: 5 residues within 4Å: Chain V: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.39: 5 residues within 4Å: Chain W: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.40: 5 residues within 4Å: Chain X: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins from Gram-Negative Bacteria. J. Mol. Biol. (2016)

Release Date

2016-07-27

Peptides

Bacterial non-heme ferritin: 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

Bacterial non-heme ferritin

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