SMTL ID : 7k5g.1

1.95 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-28

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-24-mer

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 8 residues within 4Å: Chain A: N.148, Q.151 Chain E: N.148, Q.151 Chain J: N.148, Q.151 Chain K: N.148, Q.151 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 G: N.148, Q.151 Chain L: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.8: 8 residues within 4Å: Chain D: N.148, Q.151 Chain F: N.148, Q.151 Chain I: N.148, Q.151 Chain T: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.22: 8 residues within 4Å: Chain M: N.148, Q.151 Chain Q: N.148, Q.151 Chain V: N.148, Q.151 Chain W: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.25: 8 residues within 4Å: Chain N: N.148, Q.151 Chain O: N.148, Q.151 Chain S: N.148, Q.151 Chain X: N.148, Q.151 No protein-ligand interaction detected (PLIP) K.29: 8 residues within 4Å: Chain H: N.148, Q.151 Chain P: N.148, Q.151 Chain R: N.148, Q.151 Chain U: N.148, Q.151 No protein-ligand interaction detected (PLIP)

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

HEM.2: 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 S: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 19 PLIP interactions: 10 interactions with chain S, 9 interactions with chain A, Hydrophobic interactions: S:L.19, S:I.22, S:F.26, S:F.26, S:F.26, S:I.49, S:I.49, S:M.52, S:L.71, A:L.19, A:I.22, A:F.26, A:Y.45, A:I.49, A:M.52, A:A.55, A:I.59 Salt bridges: S:K.53, A: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, A.55, I.59 Chain I: 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 C, 9 interactions with chain I, Hydrophobic interactions: C:L.19, C:I.22, C:F.26, C:F.26, C:I.49, C:M.52, C:A.55, C:I.59, I:L.19, I:I.22, I:I.22, I:F.26, I:F.26, I:F.26, I:I.49, I:M.52, I:L.71 Salt bridges: C:K.53 HEM.9: 20 residues within 4Å: Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Ligands: HEM.30 18 PLIP interactions: 10 interactions with chain D, 8 interactions with chain P, Hydrophobic interactions: D:L.19, D:I.22, D:I.22, D:F.26, D:F.26, D:I.49, D:M.52, D:A.55, D:I.59, P:L.19, P:I.22, P:F.26, P:F.26, P:I.49, P:M.52, P:L.71 Salt bridges: D:K.53, P:K.53 HEM.11: 19 residues within 4Å: Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain E: 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 B, 9 interactions with chain E, Hydrophobic interactions: B:L.19, B:I.22, B:F.26, B:F.26, B:I.49, B:M.52, B:A.55, B:I.59, E:L.19, E:I.22, E:I.22, E:F.26, E:F.26, E:I.49, E:M.52, E:L.71 Salt bridges: B:K.53, E:K.53 HEM.14: 17 residues within 4Å: Chain H: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, L.71 17 PLIP interactions: 8 interactions with chain H, 9 interactions with chain J, Hydrophobic interactions: H:L.19, H:I.22, H:F.26, H:F.26, H:I.49, H:M.52, H:I.59, J:L.19, J:I.22, J:I.22, J:F.26, J:F.26, J:I.49, J:I.49, J:M.52, J:L.71 Salt bridges: H:K.53 HEM.18: 18 residues within 4Å: Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, 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: 9 interactions with chain K, 8 interactions with chain F, Hydrophobic interactions: K:L.19, K:I.22, K:F.26, K:F.26, K:Y.45, K:I.49, K:M.52, K:L.71, F:L.19, F:F.26, F:F.26, F:I.49, F:I.49, F:M.52, F:A.55, F:I.59 Salt bridges: K:K.53 HEM.20: 20 residues within 4Å: Chain L: 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 Ligands: HEM.41 17 PLIP interactions: 7 interactions with chain X, 10 interactions with chain L, Hydrophobic interactions: X:L.19, X:F.26, X:F.26, X:I.49, X:M.52, X:L.71, L:L.19, L:I.22, L:I.22, L:F.26, L:F.26, L:I.49, L:M.52, L:A.55, L:I.59 Salt bridges: X:K.53, L:K.53 HEM.23: 19 residues within 4Å: Chain G: 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 19 PLIP interactions: 9 interactions with chain M, 10 interactions with chain G, Hydrophobic interactions: M:L.19, M:I.22, M:F.26, M:Y.45, M:I.49, M:M.52, M:A.55, M:I.59, G:L.19, G:I.22, G:F.26, G:F.26, G:F.26, G:I.49, G:I.49, G:M.52, G:L.71 Salt bridges: M:K.53, G:K.53 HEM.27: 19 residues within 4Å: Chain O: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain U: 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 U, 9 interactions with chain O, Hydrophobic interactions: U:L.19, U:I.22, U:I.22, U:F.26, U:F.26, U:F.26, U:I.49, U:M.52, U:L.71, O:L.19, O:I.22, O:F.26, O:F.26, O:I.49, O:M.52, O:A.55, O:I.59 Salt bridges: O:K.53 HEM.30: 20 residues within 4Å: Chain D: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain P: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Ligands: HEM.9 18 PLIP interactions: 10 interactions with chain P, 8 interactions with chain D, Hydrophobic interactions: P:L.19, P:I.22, P:I.22, P:F.26, P:F.26, P:I.49, P:M.52, P:A.55, P:I.59, D:L.19, D:I.22, D:F.26, D:F.26, D:I.49, D:M.52, D:L.71 Salt bridges: P:K.53, D:K.53 HEM.32: 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 Q: 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 Q, 9 interactions with chain N, Hydrophobic interactions: Q:L.19, Q:I.22, Q:I.22, Q:F.26, Q:F.26, Q:I.49, Q:M.52, Q:L.71, N:L.19, N:I.22, N:F.26, N:F.26, N:I.49, N:M.52, N:A.55, N:I.59 Salt bridges: Q:K.53, N:K.53 HEM.35: 17 residues within 4Å: Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, L.71 17 PLIP interactions: 8 interactions with chain T, 9 interactions with chain V, Hydrophobic interactions: T:L.19, T:I.22, T:F.26, T:F.26, T:I.49, T:M.52, T:I.59, V:L.19, V:I.22, V:I.22, V:F.26, V:F.26, V:I.49, V:I.49, V:M.52, V:L.71 Salt bridges: T:K.53 HEM.39: 18 residues within 4Å: Chain R: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, A.55, I.59 Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 17 PLIP interactions: 9 interactions with chain W, 8 interactions with chain R, Hydrophobic interactions: W:L.19, W:I.22, W:F.26, W:F.26, W:Y.45, W:I.49, W:M.52, W:L.71, R:L.19, R:F.26, R:F.26, R:I.49, R:I.49, R:M.52, R:A.55, R:I.59 Salt bridges: W:K.53 HEM.41: 20 residues within 4Å: Chain L: 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, I.59 Ligands: HEM.20 17 PLIP interactions: 7 interactions with chain L, 10 interactions with chain X, Hydrophobic interactions: L:L.19, L:F.26, L:F.26, L:I.49, L:M.52, L:L.71, X:L.19, X:I.22, X:I.22, X:F.26, X:F.26, X:I.49, X:M.52, X:A.55, X:I.59 Salt bridges: L:K.53, X:K.53

22 x VXS: 4-{[3-(2-hydroxyphenyl)propyl]amino}-1H-isoindole-1,3(2H)-dione(Non-covalent)

VXS.3: 9 residues within 4Å: Chain A: L.68, P.69, N.70, L.71, Q.72 Chain S: L.27, L.77, I.79, E.81 6 PLIP interactions: 2 interactions with chain S, 4 interactions with chain A Hydrophobic interactions: S:I.79, S:I.79, A:L.68 Hydrogen bonds: A:P.69, A:L.71, A:Q.72 VXS.5: 12 residues within 4Å: Chain B: L.68, P.69, N.70, L.71, Q.72 Chain E: L.27, M.31, W.35, L.77, I.79, G.80, E.81 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain E Hydrophobic interactions: B:L.68, E:W.35, E:I.79, E:I.79, E:E.81, E:E.81 Hydrogen bonds: B:P.69, B:L.71, B:Q.72 VXS.7: 10 residues within 4Å: Chain C: L.68, P.69, N.70, L.71, Q.72 Chain I: L.27, L.77, I.79, G.80, E.81 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain I Hydrogen bonds: C:P.69, C:L.71, C:Q.72 Hydrophobic interactions: I:I.79, I:I.79, I:E.81 VXS.10: 9 residues within 4Å: Chain D: L.68, P.69, N.70, L.71, Q.72 Chain P: L.27, L.77, I.79, E.81 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain P Hydrophobic interactions: D:L.68, P:I.79, P:I.79, P:E.81 Hydrogen bonds: D:P.69, D:L.71, D:Q.72 VXS.12: 12 residues within 4Å: Chain B: L.27, M.31, W.35, L.77, I.79, G.80, E.81 Chain E: L.68, P.69, N.70, L.71, Q.72 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:W.35, B:I.79, B:I.79, B:E.81, B:E.81 Hydrogen bonds: E:P.69, E:L.71, E:Q.72 VXS.13: 12 residues within 4Å: Chain F: L.68, P.69, N.70, L.71, Q.72 Chain K: L.27, M.31, W.35, L.77, I.79, G.80, E.81 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain K Hydrogen bonds: F:P.69, F:L.71, F:Q.72 Hydrophobic interactions: K:W.35, K:I.79, K:I.79, K:E.81 VXS.15: 10 residues within 4Å: Chain H: L.68, P.69, N.70, L.71, Q.72 Chain J: L.27, M.31, L.77, I.79, G.80 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain J Hydrophobic interactions: H:L.68, J:I.79, J:I.79, J:I.79 Hydrogen bonds: H:P.69, H:L.71, H:Q.72 VXS.16: 12 residues within 4Å: Chain C: L.27, M.31, W.35, L.77, I.79, G.80, E.81 Chain I: L.68, P.69, N.70, L.71, Q.72 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain I Hydrophobic interactions: C:W.35, C:I.79, C:I.79, C:E.81, I:L.68 Hydrogen bonds: I:P.69, I:L.71, I:Q.72 VXS.17: 12 residues within 4Å: Chain H: L.27, M.31, W.35, L.77, I.79, G.80, E.81 Chain J: L.68, P.69, N.70, L.71, Q.72 9 PLIP interactions: 4 interactions with chain J, 5 interactions with chain H Hydrophobic interactions: J:L.68, H:W.35, H:I.79, H:I.79, H:E.81, H:E.81 Hydrogen bonds: J:P.69, J:L.71, J:Q.72 VXS.19: 11 residues within 4Å: Chain F: L.27, M.31, L.77, I.79, G.80, E.81 Chain K: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain K Hydrophobic interactions: F:I.79, F:I.79, F:E.81 Hydrogen bonds: K:P.69, K:L.71, K:Q.72 VXS.21: 8 residues within 4Å: Chain L: L.68, P.69, N.70, L.71, Q.72 Chain X: L.27, L.77, I.79 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain X Hydrogen bonds: L:P.69, L:L.71, L:Q.72 Hydrophobic interactions: X:I.79, X:I.79 VXS.24: 9 residues within 4Å: Chain G: L.27, L.77, I.79, E.81 Chain M: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 4 interactions with chain M, 2 interactions with chain G Hydrophobic interactions: M:L.68, G:I.79, G:I.79 Hydrogen bonds: M:P.69, M:L.71, M:Q.72 VXS.26: 12 residues within 4Å: Chain N: L.68, P.69, N.70, L.71, Q.72 Chain Q: L.27, M.31, W.35, L.77, I.79, G.80, E.81 9 PLIP interactions: 4 interactions with chain N, 5 interactions with chain Q Hydrophobic interactions: N:L.68, Q:W.35, Q:I.79, Q:I.79, Q:E.81, Q:E.81 Hydrogen bonds: N:P.69, N:L.71, N:Q.72 VXS.28: 10 residues within 4Å: Chain O: L.68, P.69, N.70, L.71, Q.72 Chain U: L.27, L.77, I.79, G.80, E.81 6 PLIP interactions: 3 interactions with chain O, 3 interactions with chain U Hydrogen bonds: O:P.69, O:L.71, O:Q.72 Hydrophobic interactions: U:I.79, U:I.79, U:E.81 VXS.31: 9 residues within 4Å: Chain D: L.27, L.77, I.79, E.81 Chain P: L.68, P.69, N.70, L.71, Q.72 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain P Hydrophobic interactions: D:I.79, D:I.79, D:E.81, P:L.68 Hydrogen bonds: P:P.69, P:L.71, P:Q.72 VXS.33: 12 residues within 4Å: Chain N: L.27, M.31, W.35, L.77, I.79, G.80, E.81 Chain Q: L.68, P.69, N.70, L.71, Q.72 8 PLIP interactions: 5 interactions with chain N, 3 interactions with chain Q Hydrophobic interactions: N:W.35, N:I.79, N:I.79, N:E.81, N:E.81 Hydrogen bonds: Q:P.69, Q:L.71, Q:Q.72 VXS.34: 12 residues within 4Å: Chain R: L.68, P.69, N.70, L.71, Q.72 Chain W: L.27, M.31, W.35, L.77, I.79, G.80, E.81 7 PLIP interactions: 4 interactions with chain W, 3 interactions with chain R Hydrophobic interactions: W:W.35, W:I.79, W:I.79, W:E.81 Hydrogen bonds: R:P.69, R:L.71, R:Q.72 VXS.36: 10 residues within 4Å: Chain T: L.68, P.69, N.70, L.71, Q.72 Chain V: L.27, M.31, L.77, I.79, G.80 7 PLIP interactions: 4 interactions with chain T, 3 interactions with chain V Hydrophobic interactions: T:L.68, V:I.79, V:I.79, V:I.79 Hydrogen bonds: T:P.69, T:L.71, T:Q.72 VXS.37: 12 residues within 4Å: Chain O: L.27, M.31, W.35, L.77, I.79, G.80, E.81 Chain U: L.68, P.69, N.70, L.71, Q.72 8 PLIP interactions: 4 interactions with chain U, 4 interactions with chain O Hydrophobic interactions: U:L.68, O:W.35, O:I.79, O:I.79, O:E.81 Hydrogen bonds: U:P.69, U:L.71, U:Q.72 VXS.38: 12 residues within 4Å: Chain T: L.27, M.31, W.35, L.77, I.79, G.80, E.81 Chain V: L.68, P.69, N.70, L.71, Q.72 9 PLIP interactions: 4 interactions with chain V, 5 interactions with chain T Hydrophobic interactions: V:L.68, T:W.35, T:I.79, T:I.79, T:E.81, T:E.81 Hydrogen bonds: V:P.69, V:L.71, V:Q.72 VXS.40: 11 residues within 4Å: Chain R: L.27, M.31, L.77, I.79, G.80, E.81 Chain W: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 3 interactions with chain R, 3 interactions with chain W Hydrophobic interactions: R:I.79, R:I.79, R:E.81 Hydrogen bonds: W:P.69, W:L.71, W:Q.72 VXS.42: 8 residues within 4Å: Chain L: L.27, L.77, I.79 Chain X: L.68, P.69, N.70, L.71, Q.72 5 PLIP interactions: 3 interactions with chain X, 2 interactions with chain L Hydrogen bonds: X:P.69, X:L.71, X:Q.72 Hydrophobic interactions: L:I.79, L:I.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soldano, A. et al., Small Molecule Inhibitors of the Bacterioferritin (BfrB)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells. Acs Infect Dis. (2021)

Release Date

2020-12-16

Peptides

Ferroxidase: 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

Ferroxidase

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