SMTL ID : 4e6k.1

2.0 A resolution structure of Pseudomonas aeruginosa bacterioferritin (BfrB) in complex with bacterioferritin associated ferredoxin (Bfd)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-24-12-mer

Ligands

12 x K: POTASSIUM ION(Non-covalent)

K.1: 11 residues within 4Å: Chain 1: N.148, Q.151 Chain A: N.148, Q.151 Chain J: N.148, Q.151 Chain S: N.148, Q.151 Ligands: K.17, K.33, K.49 No protein-ligand interaction detected (PLIP) K.4: 8 residues within 4Å: Chain B: N.148, Q.151 Chain C: N.148, Q.151 Chain E: N.148, Q.151 Chain V: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.11: 11 residues within 4Å: Chain 6: N.148, Q.151 Chain F: N.148, Q.151 Chain O: N.148, Q.151 Chain X: N.148, Q.151 Ligands: K.27, K.43, K.59 No protein-ligand interaction detected (PLIP) K.17: 11 residues within 4Å: Chain 1: N.148, Q.151 Chain A: N.148, Q.151 Chain J: N.148, Q.151 Chain S: N.148, Q.151 Ligands: K.1, K.33, K.49 No protein-ligand interaction detected (PLIP) K.20: 8 residues within 4Å: Chain 4: N.148, Q.151 Chain K: N.148, Q.151 Chain L: N.148, Q.151 Chain N: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.27: 11 residues within 4Å: Chain 6: N.148, Q.151 Chain F: N.148, Q.151 Chain O: N.148, Q.151 Chain X: N.148, Q.151 Ligands: K.11, K.43, K.59 No protein-ligand interaction detected (PLIP) K.33: 11 residues within 4Å: Chain 1: N.148, Q.151 Chain A: N.148, Q.151 Chain J: N.148, Q.151 Chain S: N.148, Q.151 Ligands: K.1, K.17, K.49 No protein-ligand interaction detected (PLIP) K.36: 8 residues within 4Å: Chain M: N.148, Q.151 Chain T: N.148, Q.151 Chain U: N.148, Q.151 Chain W: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.43: 11 residues within 4Å: Chain 6: N.148, Q.151 Chain F: N.148, Q.151 Chain O: N.148, Q.151 Chain X: N.148, Q.151 Ligands: K.11, K.27, K.59 No protein-ligand interaction detected (PLIP) K.49: 11 residues within 4Å: Chain 1: N.148, Q.151 Chain A: N.148, Q.151 Chain J: N.148, Q.151 Chain S: N.148, Q.151 Ligands: K.1, K.17, K.33 No protein-ligand interaction detected (PLIP) K.52: 8 residues within 4Å: Chain 2: N.148, Q.151 Chain 3: N.148, Q.151 Chain 5: N.148, Q.151 Chain D: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.59: 11 residues within 4Å: Chain 6: N.148, Q.151 Chain F: N.148, Q.151 Chain O: N.148, Q.151 Chain X: N.148, Q.151 Ligands: K.11, K.27, K.43 No protein-ligand interaction detected (PLIP)

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

HEM.2: 18 residues within 4Å: Chain A: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:L.19, A:I.22, A:I.22, A:F.26, A:F.26, A:I.49, A:M.52, A:I.59, B:L.19, B:I.22, B:F.26, B:I.49, B:M.52, B:L.71 Water bridges: A:K.53 Salt bridges: A:K.53, B:K.53 HEM.6: 19 residues within 4Å: Chain C: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 10 interactions with chain C, 10 interactions with chain D, Hydrophobic interactions: C:L.19, C:I.22, C:F.26, C:F.26, C:I.49, C:M.52, C:L.71, D:L.19, D:I.22, D:F.26, D:F.26, D:I.49, D:I.49, D:M.52, D:A.55, D:I.59 Water bridges: C:K.53, C:K.53 Salt bridges: C:K.53, D:K.53 HEM.9: 19 residues within 4Å: Chain E: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 20 PLIP interactions: 12 interactions with chain F, 8 interactions with chain E, Hydrophobic interactions: F:L.19, F:I.22, F:I.22, F:F.26, F:F.26, F:F.26, F:I.49, F:I.49, F:M.52, F:L.71, E:L.19, E:F.26, E:F.26, E:I.49, E:M.52, E:A.55, E:I.59 Water bridges: F:K.53 Salt bridges: F:K.53, E:K.53 HEM.18: 18 residues within 4Å: Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Chain K: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 17 PLIP interactions: 10 interactions with chain J, 7 interactions with chain K, Hydrophobic interactions: J:L.19, J:I.22, J:I.22, J:F.26, J:F.26, J:I.49, J:M.52, J:I.59, K:L.19, K:I.22, K:F.26, K:I.49, K:M.52, K:L.71 Water bridges: J:K.53 Salt bridges: J:K.53, K:K.53 HEM.22: 19 residues within 4Å: Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain M: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 10 interactions with chain L, 10 interactions with chain M, Hydrophobic interactions: L:L.19, L:I.22, L:F.26, L:F.26, L:I.49, L:M.52, L:L.71, M:L.19, M:I.22, M:F.26, M:F.26, M:I.49, M:I.49, M:M.52, M:A.55, M:I.59 Water bridges: L:K.53, L:K.53 Salt bridges: L:K.53, M:K.53 HEM.25: 19 residues within 4Å: Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain O: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 20 PLIP interactions: 8 interactions with chain N, 12 interactions with chain O, Hydrophobic interactions: N:L.19, N:F.26, N:F.26, N:I.49, N:M.52, N:A.55, N:I.59, O:L.19, O:I.22, O:I.22, O:F.26, O:F.26, O:F.26, O:I.49, O:I.49, O:M.52, O:L.71 Salt bridges: N:K.53, O:K.53 Water bridges: O:K.53 HEM.34: 18 residues within 4Å: Chain S: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 17 PLIP interactions: 7 interactions with chain T, 10 interactions with chain S, Hydrophobic interactions: T:L.19, T:I.22, T:F.26, T:I.49, T:M.52, T:L.71, S:L.19, S:I.22, S:I.22, S:F.26, S:F.26, S:I.49, S:M.52, S:I.59 Salt bridges: T:K.53, S:K.53 Water bridges: S:K.53 HEM.38: 19 residues within 4Å: Chain U: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 10 interactions with chain U, 10 interactions with chain V, Hydrophobic interactions: U:L.19, U:I.22, U:F.26, U:F.26, U:I.49, U:M.52, U:L.71, V:L.19, V:I.22, V:F.26, V:F.26, V:I.49, V:I.49, V:M.52, V:A.55, V:I.59 Water bridges: U:K.53, U:K.53 Salt bridges: U:K.53, V:K.53 HEM.41: 19 residues within 4Å: Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 20 PLIP interactions: 8 interactions with chain W, 12 interactions with chain X, Hydrophobic interactions: W:L.19, 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:I.22, X:F.26, X:F.26, X:F.26, X:I.49, X:I.49, X:M.52, X:L.71 Salt bridges: W:K.53, X:K.53 Water bridges: X:K.53 HEM.50: 18 residues within 4Å: Chain 1: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Chain 2: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 17 PLIP interactions: 7 interactions with chain 2, 10 interactions with chain 1, Hydrophobic interactions: 2:L.19, 2:I.22, 2:F.26, 2:I.49, 2:M.52, 2:L.71, 1:L.19, 1:I.22, 1:I.22, 1:F.26, 1:F.26, 1:I.49, 1:M.52, 1:I.59 Salt bridges: 2:K.53, 1:K.53 Water bridges: 1:K.53 HEM.54: 19 residues within 4Å: Chain 3: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain 4: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 20 PLIP interactions: 10 interactions with chain 3, 10 interactions with chain 4, Hydrophobic interactions: 3:L.19, 3:I.22, 3:F.26, 3:F.26, 3:I.49, 3:M.52, 3:L.71, 4:L.19, 4:I.22, 4:F.26, 4:F.26, 4:I.49, 4:I.49, 4:M.52, 4:A.55, 4:I.59 Water bridges: 3:K.53, 3:K.53 Salt bridges: 3:K.53, 4:K.53 HEM.57: 19 residues within 4Å: Chain 5: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain 6: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 20 PLIP interactions: 12 interactions with chain 6, 8 interactions with chain 5, Hydrophobic interactions: 6:L.19, 6:I.22, 6:I.22, 6:F.26, 6:F.26, 6:F.26, 6:I.49, 6:I.49, 6:M.52, 6:L.71, 5:L.19, 5:F.26, 5:F.26, 5:I.49, 5:M.52, 5:A.55, 5:I.59 Water bridges: 6:K.53 Salt bridges: 6:K.53, 5:K.53

24 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: D.132, T.136 Chain S: D.34 Ligand excluded by PLIP NA.5: 3 residues within 4Å: Chain B: D.132, T.136 Chain C: D.34 Ligand excluded by PLIP NA.7: 3 residues within 4Å: Chain C: D.132, T.136 Chain E: D.34 Ligand excluded by PLIP NA.8: 3 residues within 4Å: Chain 2: D.34 Chain D: D.132, T.136 Ligand excluded by PLIP NA.10: 3 residues within 4Å: Chain E: D.132, T.136 Chain V: D.34 Ligand excluded by PLIP NA.12: 3 residues within 4Å: Chain 6: D.34 Chain F: D.132, T.136 Ligand excluded by PLIP NA.19: 3 residues within 4Å: Chain 1: D.34 Chain J: D.132, T.136 Ligand excluded by PLIP NA.21: 3 residues within 4Å: Chain K: D.132, T.136 Chain L: D.34 Ligand excluded by PLIP NA.23: 3 residues within 4Å: Chain L: D.132, T.136 Chain N: D.34 Ligand excluded by PLIP NA.24: 3 residues within 4Å: Chain M: D.132, T.136 Chain T: D.34 Ligand excluded by PLIP NA.26: 3 residues within 4Å: Chain 4: D.34 Chain N: D.132, T.136 Ligand excluded by PLIP NA.28: 3 residues within 4Å: Chain O: D.132, T.136 Chain X: D.34 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain J: D.34 Chain S: D.132, T.136 Ligand excluded by PLIP NA.37: 3 residues within 4Å: Chain T: D.132, T.136 Chain U: D.34 Ligand excluded by PLIP NA.39: 3 residues within 4Å: Chain U: D.132, T.136 Chain W: D.34 Ligand excluded by PLIP NA.40: 3 residues within 4Å: Chain B: D.34 Chain V: D.132, T.136 Ligand excluded by PLIP NA.42: 3 residues within 4Å: Chain M: D.34 Chain W: D.132, T.136 Ligand excluded by PLIP NA.44: 3 residues within 4Å: Chain F: D.34 Chain X: D.132, T.136 Ligand excluded by PLIP NA.51: 3 residues within 4Å: Chain 1: D.132, T.136 Chain A: D.34 Ligand excluded by PLIP NA.53: 3 residues within 4Å: Chain 2: D.132, T.136 Chain 3: D.34 Ligand excluded by PLIP NA.55: 3 residues within 4Å: Chain 3: D.132, T.136 Chain 5: D.34 Ligand excluded by PLIP NA.56: 3 residues within 4Å: Chain 4: D.132, T.136 Chain K: D.34 Ligand excluded by PLIP NA.58: 3 residues within 4Å: Chain 5: D.132, T.136 Chain D: D.34 Ligand excluded by PLIP NA.60: 3 residues within 4Å: Chain 6: D.132, T.136 Chain O: D.34 Ligand excluded by PLIP

12 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.13: 10 residues within 4Å: Chain B: Q.72 Chain G: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.4, G:C.6, G:C.38, G:C.41 FES.15: 9 residues within 4Å: Chain C: Q.72 Chain H: C.4, L.5, C.6, G.35, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.4, H:C.6, H:C.38, H:C.41 FES.16: 10 residues within 4Å: Chain E: Q.72 Chain I: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.4, I:C.6, I:C.38, I:C.41 FES.29: 10 residues within 4Å: Chain K: Q.72 Chain P: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain P, Metal complexes: P:C.4, P:C.6, P:C.38, P:C.41 FES.31: 9 residues within 4Å: Chain L: Q.72 Chain Q: C.4, L.5, C.6, G.35, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain Q, Metal complexes: Q:C.4, Q:C.6, Q:C.38, Q:C.41 FES.32: 10 residues within 4Å: Chain N: Q.72 Chain R: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain R, Metal complexes: R:C.4, R:C.6, R:C.38, R:C.41 FES.45: 10 residues within 4Å: Chain T: Q.72 Chain Y: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain Y, Metal complexes: Y:C.4, Y:C.6, Y:C.38, Y:C.41 FES.47: 9 residues within 4Å: Chain U: Q.72 Chain Z: C.4, L.5, C.6, G.35, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain Z, Metal complexes: Z:C.4, Z:C.6, Z:C.38, Z:C.41 FES.48: 10 residues within 4Å: Chain 0: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 Chain W: Q.72 4 PLIP interactions: 4 interactions with chain 0, Metal complexes: 0:C.4, 0:C.6, 0:C.38, 0:C.41 FES.61: 10 residues within 4Å: Chain 2: Q.72 Chain 7: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain 7, Metal complexes: 7:C.4, 7:C.6, 7:C.38, 7:C.41 FES.63: 9 residues within 4Å: Chain 3: Q.72 Chain 8: C.4, L.5, C.6, G.35, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain 8, Metal complexes: 8:C.4, 8:C.6, 8:C.38, 8:C.41 FES.64: 10 residues within 4Å: Chain 5: Q.72 Chain 9: C.4, L.5, C.6, G.35, T.36, Q.37, C.38, G.39, C.41 4 PLIP interactions: 4 interactions with chain 9, Metal complexes: 9:C.4, 9:C.6, 9:C.38, 9:C.41

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.14: 4 residues within 4Å: Chain G: Y.25, R.26, R.29, K.46 6 PLIP interactions: 6 interactions with chain G Water bridges: G:R.29, G:R.29, G:K.46 Salt bridges: G:R.26, G:R.29, G:K.46 PO4.30: 4 residues within 4Å: Chain P: Y.25, R.26, R.29, K.46 6 PLIP interactions: 6 interactions with chain P Water bridges: P:R.29, P:R.29, P:K.46 Salt bridges: P:R.26, P:R.29, P:K.46 PO4.46: 4 residues within 4Å: Chain Y: Y.25, R.26, R.29, K.46 6 PLIP interactions: 6 interactions with chain Y Water bridges: Y:R.29, Y:R.29, Y:K.46 Salt bridges: Y:R.26, Y:R.29, Y:K.46 PO4.62: 4 residues within 4Å: Chain 7: Y.25, R.26, R.29, K.46 6 PLIP interactions: 6 interactions with chain 7 Water bridges: 7:R.29, 7:R.29, 7:K.46 Salt bridges: 7:R.26, 7:R.29, 7:K.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, H. et al., The Structure of the BfrB-Bfd Complex Reveals Protein-Protein Interactions Enabling Iron Release from Bacterioferritin. J.Am.Chem.Soc. (2012)

Release Date

2012-08-01

Peptides

Bacterioferritin: ABCDEFJKLMNOSTUVWX123456
bacterioferritin-associated ferredoxin: GHIPQRYZ0789

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

J
A

K
B

L
C

M
D

N
E

O
F

S
A

T
B

U
C

V
D

W
E

X
F

1
A

2
B

3
C

4
D

5
E

6
F

G
G

H
H

I
I

P
G

Q
H

R
I

Y
G

Z
H

0
I

7
G

8
H

9
I

Bacterioferritin

bacterioferritin-associated ferredoxin

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