SMTL ID : 5c6f.1 (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

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

FE.1: 5 residues within 4Å: Chain A: H.155 Chain B: H.155 Chain D: H.155 Chain O: H.155 Ligands: FE.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.155 FE.2: 5 residues within 4Å: Chain A: H.155 Chain D: H.155 Chain O: H.155, L.159 Ligands: FE.1 No protein-ligand interaction detected (PLIP) FE.3: 4 residues within 4Å: Chain A: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.56, A:E.100, A:E.136, H2O.3 FE.5: 5 residues within 4Å: Chain B: H.52, E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.56, B:E.100, B:E.136, H2O.10 FE.10: 3 residues within 4Å: Ligands: FE.20, FE.30, FE.40 No protein-ligand interaction detected (PLIP) FE.11: 5 residues within 4Å: Chain G: H.155 Chain H: H.155 Chain J: H.155 Chain U: H.155 Ligands: FE.12 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:H.155 FE.12: 5 residues within 4Å: Chain G: H.155 Chain J: H.155 Chain U: H.155, L.159 Ligands: FE.11 No protein-ligand interaction detected (PLIP) FE.13: 4 residues within 4Å: Chain G: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.56, G:E.100, G:E.136, H2O.46 FE.15: 5 residues within 4Å: Chain H: H.52, E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.56, H:E.100, H:E.136, H2O.54 FE.20: 3 residues within 4Å: Ligands: FE.10, FE.30, FE.40 No protein-ligand interaction detected (PLIP) FE.21: 5 residues within 4Å: Chain I: H.155 Chain M: H.155 Chain N: H.155 Chain P: H.155 Ligands: FE.22 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:H.155 FE.22: 5 residues within 4Å: Chain I: H.155, L.159 Chain M: H.155 Chain P: H.155 Ligands: FE.21 No protein-ligand interaction detected (PLIP) FE.23: 4 residues within 4Å: Chain M: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:E.56, M:E.100, M:E.136, H2O.89 FE.25: 5 residues within 4Å: Chain N: H.52, E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:E.56, N:E.100, N:E.136, H2O.97 FE.30: 3 residues within 4Å: Ligands: FE.10, FE.20, FE.40 No protein-ligand interaction detected (PLIP) FE.31: 5 residues within 4Å: Chain C: H.155 Chain S: H.155 Chain T: H.155 Chain V: H.155 Ligands: FE.32 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:H.155 FE.32: 5 residues within 4Å: Chain C: H.155, L.159 Chain S: H.155 Chain V: H.155 Ligands: FE.31 No protein-ligand interaction detected (PLIP) FE.33: 4 residues within 4Å: Chain S: E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: S:E.56, S:E.100, S:E.136, H2O.133 FE.35: 5 residues within 4Å: Chain T: H.52, E.56, E.100, Q.133, E.136 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:E.56, T:E.100, T:E.136, H2O.140 FE.40: 3 residues within 4Å: Ligands: FE.10, FE.20, FE.30 No protein-ligand interaction detected (PLIP)

20 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.6: 5 residues within 4Å: Chain B: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.7: 5 residues within 4Å: Chain C: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.8: 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.14: 5 residues within 4Å: Chain G: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.16: 5 residues within 4Å: Chain H: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.17: 5 residues within 4Å: Chain I: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.18: 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.24: 5 residues within 4Å: Chain M: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.26: 5 residues within 4Å: Chain N: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.27: 5 residues within 4Å: Chain O: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.28: 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.34: 5 residues within 4Å: Chain S: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.36: 5 residues within 4Å: Chain T: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.37: 5 residues within 4Å: Chain U: H.59, K.62, F.125, Y.129, E.132 Ligand excluded by PLIP IMD.38: 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

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
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

Bacterial non-heme ferritin

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