SMTL ID : 3ise.1

Structure of mineralized Bfrb (double soak) from Pseudomonas aeruginosa to 2.8A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-24-mer

Ligands

24 x FE: FE (III) ION(Non-covalent)

FE.1: 3 residues within 4Å: Chain A: H.153 Chain X: M.154, H.155 2 PLIP interactions: 1 interactions with chain X, 1 interactions with chain A Metal complexes: X:H.155, A:H.153 FE.2: 3 residues within 4Å: Chain A: M.154, H.155 Chain L: H.153 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain A Metal complexes: L:H.153, A:H.155 FE.5: 3 residues within 4Å: Chain B: H.155 Chain H: R.39, H.153 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B Metal complexes: H:H.153, B:H.155 FE.6: 2 residues within 4Å: Chain B: H.153 Chain D: H.155 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.155, B:H.153 FE.8: 3 residues within 4Å: Chain C: M.154, H.155 Chain U: H.153 2 PLIP interactions: 1 interactions with chain U, 1 interactions with chain C Metal complexes: U:H.153, C:H.155 FE.11: 3 residues within 4Å: Chain D: R.39, H.153 Chain F: H.155 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Metal complexes: D:H.153, F:H.155 FE.13: 3 residues within 4Å: Chain E: M.154, H.155 Chain J: H.153 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain E Metal complexes: J:H.153, E:H.155 FE.14: 3 residues within 4Å: Chain F: R.39, H.153 Chain H: H.155 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain F Metal complexes: H:H.155, F:H.153 FE.15: 4 residues within 4Å: Chain G: R.39, H.153 Chain I: M.154, H.155 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain G Metal complexes: I:H.155, G:H.153 FE.16: 3 residues within 4Å: Chain G: M.154, H.155 Chain W: H.153 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain W Metal complexes: G:H.155, W:H.153 FE.19: 3 residues within 4Å: Chain I: R.39, H.153 Chain O: H.155 2 PLIP interactions: 1 interactions with chain O, 1 interactions with chain I Metal complexes: O:H.155, I:H.153 FE.21: 3 residues within 4Å: Chain C: R.39, H.153 Chain K: H.155 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain C Metal complexes: K:H.155, C:H.153 FE.22: 2 residues within 4Å: Chain K: H.153 Chain S: H.155 2 PLIP interactions: 1 interactions with chain S, 1 interactions with chain K Metal complexes: S:H.155, K:H.153 FE.24: 3 residues within 4Å: Chain L: M.154, H.155 Chain M: H.153 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain M Metal complexes: L:H.155, M:H.153 FE.26: 3 residues within 4Å: Chain M: H.155 Chain X: R.39, H.153 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain X Metal complexes: M:H.155, X:H.153 FE.27: 3 residues within 4Å: Chain N: M.154, H.155 Chain T: H.153 2 PLIP interactions: 1 interactions with chain T, 1 interactions with chain N Metal complexes: T:H.153, N:H.155 FE.30: 4 residues within 4Å: Chain N: R.39, H.153 Chain P: M.154, H.155 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain N Metal complexes: P:H.155, N:H.153 FE.31: 3 residues within 4Å: Chain P: R.39, H.153 Chain R: H.155 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain R Metal complexes: P:H.153, R:H.155 FE.32: 4 residues within 4Å: Chain J: M.154, H.155 Chain Q: R.39, H.153 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain J Metal complexes: Q:H.153, J:H.155 FE.35: 3 residues within 4Å: Chain R: Q.137, H.153 Chain T: H.155 2 PLIP interactions: 1 interactions with chain R, 1 interactions with chain T Metal complexes: R:H.153, T:H.155 FE.37: 4 residues within 4Å: Chain S: Q.137, H.153 Chain U: M.154, H.155 2 PLIP interactions: 1 interactions with chain S, 1 interactions with chain U Metal complexes: S:H.153, U:H.155 FE.38: 4 residues within 4Å: Chain Q: M.154, H.155 Chain V: Q.137, H.153 2 PLIP interactions: 1 interactions with chain V, 1 interactions with chain Q Metal complexes: V:H.153, Q:H.155 FE.39: 2 residues within 4Å: Chain E: H.153 Chain V: H.155 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain V Metal complexes: E:H.153, V:H.155 FE.42: 4 residues within 4Å: Chain O: R.39, H.153 Chain W: M.154, H.155 2 PLIP interactions: 1 interactions with chain W, 1 interactions with chain O Metal complexes: W:H.155, O:H.153

6 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: N.148, Q.151 Chain L: N.148, Q.151 Chain M: N.148, Q.151 Chain X: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.7: 8 residues within 4Å: Chain B: N.148, Q.151 Chain D: N.148, Q.151 Chain F: N.148, Q.151 Chain H: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.9: 8 residues within 4Å: Chain C: N.148, Q.151 Chain K: N.148, Q.151 Chain S: N.148, Q.151 Chain U: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.17: 8 residues within 4Å: Chain G: N.148, Q.151 Chain I: N.148, Q.151 Chain O: N.148, Q.151 Chain W: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.28: 8 residues within 4Å: Chain N: N.148, Q.151 Chain P: N.148, Q.151 Chain R: N.148, Q.151 Chain T: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.40: 8 residues within 4Å: Chain E: N.148, Q.151 Chain J: N.148, Q.151 Chain Q: N.148, Q.151 Chain V: N.148, Q.151 No protein-ligand interaction detected (PLIP)

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

HEM.4: 19 residues within 4Å: Chain A: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B, Hydrophobic interactions: A:L.19, A:I.22, A:I.22, A:F.26, A:I.49, A:M.52, A:A.55, A:I.59, B:L.19, B:I.22, B:F.26, B:F.26, B:F.26, B:F.26, B:M.52, B:L.71 Salt bridges: A:K.53, B:K.53 HEM.10: 15 residues within 4Å: Chain C: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain D: L.19, N.23, F.26, Y.45, I.49, M.52, K.53 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain D, Hydrophobic interactions: C:L.19, C:I.22, C:I.22, C:F.26, C:F.26, C:Y.45, C:I.49, C:I.49, C:M.52, D:L.19, D:F.26, D:F.26, D:F.26, D:I.49, D:I.49, D:M.52 Salt bridges: C:K.53, D:K.53 HEM.12: 17 residues within 4Å: Chain E: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 17 PLIP interactions: 8 interactions with chain E, 9 interactions with chain F, Hydrophobic interactions: E:L.19, E:I.22, E:I.22, E:F.26, E:F.26, E:I.49, E:M.52, F:L.19, F:I.22, F:F.26, F:F.26, F:F.26, F:I.49, F:M.52, F:L.71 Salt bridges: E:K.53, F:K.53 HEM.18: 17 residues within 4Å: Chain G: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55 Chain H: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 15 PLIP interactions: 7 interactions with chain G, 8 interactions with chain H, Hydrophobic interactions: G:L.19, G:F.26, G:F.26, G:I.49, G:M.52, G:A.55, H:L.19, H:I.22, H:I.22, H:F.26, H:F.26, H:I.49, H:M.52 Salt bridges: G:K.53, H:K.53 HEM.20: 16 residues within 4Å: Chain I: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 13 PLIP interactions: 7 interactions with chain J, 6 interactions with chain I, Hydrophobic interactions: J:L.19, J:I.22, J:F.26, J:F.26, J:I.49, J:M.52, I:L.19, I:I.22, I:F.26, I:F.26, I:M.52 Salt bridges: J:K.53, I:K.53 HEM.23: 18 residues within 4Å: Chain K: I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55 17 PLIP interactions: 10 interactions with chain L, 7 interactions with chain K, Hydrophobic interactions: L:L.19, L:I.22, L:I.22, L:F.26, L:F.26, L:F.26, L:I.49, L:M.52, L:A.55, K:I.22, K:F.26, K:F.26, K:I.49, K:M.52, K:A.55 Salt bridges: L:K.53, K:K.53 HEM.25: 16 residues within 4Å: Chain M: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 14 PLIP interactions: 7 interactions with chain N, 7 interactions with chain M, Hydrophobic interactions: N:L.19, N:I.22, N:F.26, N:F.26, N:I.49, N:M.52, M:L.19, M:I.22, M:I.22, M:F.26, M:F.26, M:M.52 Salt bridges: N:K.53, M:K.53 HEM.29: 17 residues within 4Å: Chain O: L.19, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 16 PLIP interactions: 9 interactions with chain P, 7 interactions with chain O, Hydrophobic interactions: P:L.19, P:I.22, P:I.22, P:F.26, P:F.26, P:F.26, P:I.49, P:M.52, O:L.19, O:F.26, O:F.26, O:I.49, O:M.52, O:A.55 Salt bridges: P:K.53, O:K.53 HEM.33: 17 residues within 4Å: Chain Q: L.19, I.22, N.23, F.26, Y.45, I.49, M.52 Chain R: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, D.56, L.71 13 PLIP interactions: 7 interactions with chain R, 6 interactions with chain Q, Hydrophobic interactions: R:L.19, R:I.22, R:F.26, R:F.26, R:I.49, R:L.71, Q:L.19, Q:F.26, Q:F.26, Q:I.49, Q:M.52 Salt bridges: R:K.53, Q:K.53 HEM.34: 17 residues within 4Å: Chain S: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53 Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 15 PLIP interactions: 6 interactions with chain S, 9 interactions with chain T, Hydrophobic interactions: S:L.19, S:F.26, S:F.26, S:I.49, S:M.52, T:L.19, T:I.22, T:F.26, T:F.26, T:I.49, T:I.49, T:M.52, T:L.71 Salt bridges: S:K.53, T:K.53 HEM.36: 18 residues within 4Å: Chain U: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56 Chain V: I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 14 PLIP interactions: 8 interactions with chain U, 6 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:A.55, V:F.26, V:F.26, V:F.26, V:M.52, V:L.71 Salt bridges: U:K.53, V:K.53 HEM.41: 18 residues within 4Å: Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55 15 PLIP interactions: 10 interactions with chain X, 5 interactions with chain W, Hydrophobic interactions: X:L.19, X:I.22, X:I.22, X:F.26, X:F.26, X:I.49, X:I.49, X:M.52, X:A.55, W:L.19, W:F.26, W:M.52, W:L.71 Salt bridges: X:K.53, W:K.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weeratunga, S.K. et al., Structural Studies of Bacterioferritin B from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center. Biochemistry (2010)

Release Date

2010-02-02

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
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Bacterioferritin

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