SMTL ID : 3e1j.1

Crystal structure of E. coli Bacterioferritin (BFR) with an unoccupied ferroxidase centre (APO-BFR).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-24-mer

Ligands

32 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: R.117, I.121 Chain J: R.117, I.121 Chain P: R.117, I.121 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain B: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain B: R.117, I.121 Chain C: R.117, I.121 Chain H: R.117, I.121 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain C: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain D: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain E: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain F: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain F: R.117, I.121 Chain I: R.117, I.121 Chain K: R.117, I.121 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain G: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain G: R.117 Chain L: R.117, I.121 Chain Q: R.117 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain H: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain I: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain J: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain K: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain L: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain M: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain D: R.117, I.121 Chain M: R.117, I.121 Chain V: R.117, I.121 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain N: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.26: 6 residues within 4Å: Chain N: R.117, I.121 Chain O: R.117, I.121 Chain T: R.117, I.121 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain O: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain P: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain Q: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain R: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain R: R.117, I.121 Chain U: R.117, I.121 Chain W: R.117, I.121 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain S: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain E: R.117 Chain S: R.117 Chain X: R.117, I.121 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain T: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain U: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain V: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain W: G.145, L.146, Q.147 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain X: G.145, L.146, Q.147 Ligand excluded by PLIP

12 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.5: 16 residues within 4Å: Chain A: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A, Hydrophobic interactions: B:L.19, B:I.22, B:F.26, B:F.26, B:F.26, B:Y.45, B:I.49, B:I.49, B:M.52, A:I.22, A:F.26, A:F.26, A:I.49, A:I.49, A:M.52, A:A.55, A:I.59 HEM.7: 16 residues within 4Å: Chain C: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 7 interactions with chain C, 9 interactions with chain D, Hydrophobic interactions: C:I.22, C:F.26, C:I.49, C:I.49, C:M.52, C:A.55, C:I.59, D:L.19, D:I.22, D:I.22, D:F.26, D:F.26, D:Y.45, D:I.49, D:I.49, D:M.52 HEM.12: 16 residues within 4Å: Chain E: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 15 PLIP interactions: 8 interactions with chain F, 7 interactions with chain E, Hydrophobic interactions: F:L.19, F:I.22, F:F.26, F:F.26, F:Y.45, F:I.49, F:I.49, F:M.52, E:I.22, E:F.26, E:Y.45, E:I.49, E:M.52, E:A.55, E:I.59 HEM.16: 16 residues within 4Å: Chain G: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain H: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 7 interactions with chain G, 9 interactions with chain H, Hydrophobic interactions: G:I.22, G:F.26, G:I.49, G:I.49, G:M.52, G:A.55, G:I.59, H:L.19, H:I.22, H:I.22, H:F.26, H:F.26, H:Y.45, H:I.49, H:I.49, H:M.52 HEM.19: 16 residues within 4Å: Chain I: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 8 interactions with chain I, 8 interactions with chain J, Hydrophobic interactions: I:I.22, I:F.26, I:F.26, I:I.49, I:I.49, I:M.52, I:A.55, I:I.59, J:L.19, J:I.22, J:F.26, J:F.26, J:Y.45, J:I.49, J:I.49, J:M.52 HEM.22: 16 residues within 4Å: Chain K: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 15 PLIP interactions: 8 interactions with chain L, 7 interactions with chain K, Hydrophobic interactions: L:L.19, L:I.22, L:F.26, L:F.26, L:Y.45, L:I.49, L:I.49, L:M.52, K:I.22, K:F.26, K:F.26, K:I.49, K:M.52, K:A.55, K:I.59 HEM.27: 16 residues within 4Å: Chain M: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 17 PLIP interactions: 9 interactions with chain N, 8 interactions with chain M, Hydrophobic interactions: N:L.19, N:I.22, N:F.26, N:F.26, N:F.26, N:Y.45, N:I.49, N:I.49, N:M.52, M:I.22, M:F.26, M:F.26, M:I.49, M:I.49, M:M.52, M:A.55, M:I.59 HEM.29: 16 residues within 4Å: Chain O: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 7 interactions with chain O, 9 interactions with chain P, Hydrophobic interactions: O:I.22, O:F.26, O:I.49, O:I.49, O:M.52, O:A.55, O:I.59, P:L.19, P:I.22, P:I.22, P:F.26, P:F.26, P:Y.45, P:I.49, P:I.49, P:M.52 HEM.34: 16 residues within 4Å: Chain Q: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain R: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 15 PLIP interactions: 7 interactions with chain Q, 8 interactions with chain R, Hydrophobic interactions: Q:I.22, Q:F.26, Q:Y.45, Q:I.49, Q:M.52, Q:A.55, Q:I.59, R:L.19, R:I.22, R:F.26, R:F.26, R:Y.45, R:I.49, R:I.49, R:M.52 HEM.38: 16 residues within 4Å: Chain S: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 7 interactions with chain S, 9 interactions with chain T, Hydrophobic interactions: S:I.22, S:F.26, S:I.49, S:I.49, S:M.52, S:A.55, S:I.59, T:L.19, T:I.22, T:I.22, T:F.26, T:F.26, T:Y.45, T:I.49, T:I.49, T:M.52 HEM.41: 16 residues within 4Å: Chain U: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 16 PLIP interactions: 8 interactions with chain V, 8 interactions with chain U, Hydrophobic interactions: V:L.19, V:I.22, V:F.26, V:F.26, V:Y.45, V:I.49, V:I.49, V:M.52, U:I.22, U:F.26, U:F.26, U:I.49, U:I.49, U:M.52, U:A.55, U:I.59 HEM.44: 16 residues within 4Å: Chain W: I.22, N.23, F.26, Y.45, I.49, M.52, A.55, D.56, I.59 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 15 PLIP interactions: 7 interactions with chain W, 8 interactions with chain X, Hydrophobic interactions: W:I.22, W:F.26, W:F.26, W:I.49, W:M.52, W:A.55, W:I.59, X:L.19, X:I.22, X:F.26, X:F.26, X:Y.45, X:I.49, X:I.49, X:M.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crow, A. et al., Structural basis for iron mineralization by bacterioferritin. J.Am.Chem.Soc. (2009)

Release Date

2009-05-05

Peptides

Bacterioferritin: 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

Bacterioferritin

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