SMTL ID : 6nli.1

1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 11)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-24-mer

Ligands

6 x FE2: FE (II) ION(Non-covalent)

FE2.1: 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) FE2.5: 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) FE2.11: 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) FE2.33: 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) FE2.37: 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) FE2.43: 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 20 PLIP interactions: 9 interactions with chain S, 11 interactions with chain A, Hydrophobic interactions: S:L.19, S:F.26, S:I.49, S:I.49, S:M.52, S:L.71, A:L.19, A:I.22, A:I.22, A:F.26, A:F.26, A:I.49, A:M.52, A:A.55, A:I.59 Water bridges: S:K.53, S:K.53, A:K.53 Salt bridges: S:K.53, A:K.53 HEM.8: 18 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 18 PLIP interactions: 8 interactions with chain I, 10 interactions with chain C, Hydrophobic interactions: I:L.19, I:I.22, I:F.26, I:F.26, I:F.26, I:I.49, I:M.52, C:L.19, C:I.22, C:I.22, C:F.26, C:F.26, C:I.49, C:M.52, C:A.55, C:I.59 Salt bridges: I:K.53, C:K.53 HEM.12: 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.44 20 PLIP interactions: 10 interactions with chain P, 10 interactions with chain D, Hydrophobic interactions: P:L.19, P:F.26, P:F.26, P:Y.45, P:I.49, P:I.49, P:M.52, P:L.71, 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 Water bridges: P:Y.45 Salt bridges: P:K.53, D:K.53 HEM.16: 19 residues within 4Å: Chain B: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain E: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain E, Hydrophobic interactions: B:L.19, B:F.26, B:F.26, B:I.49, B:M.52, B:L.71, E:L.19, E:I.22, E:I.22, E:F.26, E:F.26, E:I.49, E:I.49, E:M.52, E:A.55, E:I.59 Salt bridges: B:K.53, E:K.53 HEM.19: 19 residues within 4Å: Chain F: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain K: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 19 PLIP interactions: 11 interactions with chain F, 8 interactions with chain K, Hydrophobic interactions: F:L.19, F:I.22, F:I.22, F:F.26, F:F.26, F:I.49, F:I.49, F:M.52, F:A.55, F:I.59, K:L.19, K:I.22, K:F.26, K:F.26, K:I.49, K:M.52, K:L.71 Salt bridges: F:K.53, K:K.53 HEM.27: 19 residues within 4Å: Chain H: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain J: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 19 PLIP interactions: 9 interactions with chain H, 10 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:A.55, H:I.59, J:L.19, J:I.22, J:I.22, J:F.26, J:F.26, J:F.26, J:I.49, J:M.52, J:L.71 Salt bridges: H:K.53, J:K.53 HEM.31: 21 residues within 4Å: Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56, L.71 Ligands: HEM.63 19 PLIP interactions: 11 interactions with chain X, 8 interactions with chain L, 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, X:L.71, L:L.19, L:I.22, L:F.26, L:F.26, L:I.49, L:M.52, L:I.59 Salt bridges: X:K.53, L:K.53 HEM.34: 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 20 PLIP interactions: 11 interactions with chain M, 9 interactions with chain G, Hydrophobic interactions: M:L.19, M:I.22, M:I.22, M:F.26, M:F.26, M:I.49, M:M.52, M:A.55, M:I.59, G:L.19, G:F.26, G:I.49, G:I.49, G:M.52, G:L.71 Water bridges: M:K.53, G:K.53, G:K.53 Salt bridges: M:K.53, G:K.53 HEM.40: 18 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 18 PLIP interactions: 8 interactions with chain U, 10 interactions with chain O, Hydrophobic interactions: U:L.19, U:I.22, U:F.26, U:F.26, U:F.26, U:I.49, U:M.52, O:L.19, O:I.22, O:I.22, O:F.26, O:F.26, O:I.49, O:M.52, O:A.55, O:I.59 Salt bridges: U:K.53, O:K.53 HEM.44: 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.12 19 PLIP interactions: 9 interactions with chain D, 10 interactions with chain P, Hydrophobic interactions: D:L.19, D:F.26, D:F.26, D:Y.45, D:I.49, D:I.49, D:M.52, D:L.71, 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 Salt bridges: D:K.53, P:K.53 HEM.48: 19 residues within 4Å: Chain N: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 Chain Q: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 18 PLIP interactions: 11 interactions with chain Q, 7 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:I.49, Q:M.52, Q:A.55, Q:I.59, N:L.19, N:F.26, N:F.26, N:I.49, N:M.52, N:L.71 Salt bridges: Q:K.53, N:K.53 HEM.51: 19 residues within 4Å: Chain R: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain W: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 19 PLIP interactions: 11 interactions with chain R, 8 interactions with chain W, Hydrophobic interactions: R:L.19, R:I.22, R:I.22, R:F.26, R:F.26, R:I.49, R:I.49, R:M.52, R:A.55, R:I.59, W:L.19, W:I.22, W:F.26, W:F.26, W:I.49, W:M.52, W:L.71 Salt bridges: R:K.53, W:K.53 HEM.59: 19 residues within 4Å: Chain T: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, I.59 Chain V: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, L.71 19 PLIP interactions: 9 interactions with chain T, 10 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:A.55, T:I.59, V:L.19, V:I.22, V:I.22, V:F.26, V:F.26, V:F.26, V:I.49, V:M.52, V:L.71 Salt bridges: T:K.53, V:K.53 HEM.63: 21 residues within 4Å: Chain L: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, A.55, D.56, L.71 Chain X: L.19, I.22, N.23, F.26, Y.45, I.49, M.52, K.53, I.59 Ligands: HEM.31 19 PLIP interactions: 11 interactions with chain L, 8 interactions with chain X, Hydrophobic interactions: L:L.19, L:I.22, L:I.22, L:F.26, L:F.26, L:I.49, L:I.49, L:M.52, L:A.55, L:L.71, X:L.19, X:I.22, X:F.26, X:F.26, X:I.49, X:M.52, X:I.59 Salt bridges: L:K.53, X:K.53

18 x KTM: 4-{[(2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione(Non-covalent)

KTM.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, G.80 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain S Hydrophobic interactions: A:L.68, S:I.79, S:I.79 Hydrogen bonds: A:P.69, A:L.71, A:Q.72 KTM.6: 9 residues within 4Å: Chain B: L.68, P.69, N.70, L.71, Q.72 Chain E: L.27, I.79, G.80, E.81 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:L.68, E:I.79, E:I.79, E:E.81 Hydrogen bonds: B:P.69, B:L.71, B:Q.72 KTM.9: 9 residues within 4Å: Chain C: L.68, P.69, N.70, L.71, Q.72 Chain I: L.27, I.79, G.80, E.81 7 PLIP interactions: 3 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: I:I.79, I:I.79, I:E.81, C:L.68 Hydrogen bonds: C:P.69, C:L.71, C:Q.72 KTM.13: 10 residues within 4Å: Chain D: L.68, P.69, N.70, L.71, Q.72 Chain P: L.27, L.77, I.79, G.80, E.81 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain P Hydrophobic interactions: D:L.68, D:L.68, P:I.79, P:I.79 Hydrogen bonds: D:P.69, D:L.71, D:Q.72 KTM.17: 11 residues within 4Å: Chain B: L.27, M.31, L.77, I.79, G.80, E.81 Chain E: L.68, P.69, N.70, L.71, Q.72 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:L.68, E:L.68, B:I.79, B:I.79 Hydrogen bonds: E:P.69, E:L.71, E:Q.72 KTM.22: 10 residues within 4Å: Chain G: L.68, P.69, N.70, L.71, Q.72 Chain M: L.27, L.77, I.79, G.80, E.81 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain M Hydrogen bonds: G:P.69, G:L.71, G:Q.72 Hydrophobic interactions: M:I.79, M:I.79, M:E.81 KTM.24: 10 residues within 4Å: Chain H: L.68, P.69, N.70, L.71, Q.72 Chain J: L.27, L.77, I.79, G.80, E.81 6 PLIP interactions: 4 interactions with chain H, 2 interactions with chain J Hydrophobic interactions: H:L.68, J:I.79, J:I.79 Hydrogen bonds: H:P.69, H:L.71, H:Q.72 KTM.26: 9 residues within 4Å: Chain C: L.27, I.79, G.80, E.81 Chain I: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain C Hydrophobic interactions: I:L.68, C:I.79, C:I.79 Hydrogen bonds: I:P.69, I:L.71, I:Q.72 KTM.28: 10 residues within 4Å: Chain H: L.27, L.77, I.79, G.80, E.81 Chain J: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 4 interactions with chain J, 2 interactions with chain H Hydrophobic interactions: J:L.68, H:I.79, H:I.79 Hydrogen bonds: J:P.69, J:L.71, J:Q.72 KTM.35: 9 residues within 4Å: Chain G: L.27, L.77, I.79, G.80 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 KTM.38: 9 residues within 4Å: Chain N: L.68, P.69, N.70, L.71, Q.72 Chain Q: L.27, I.79, G.80, E.81 7 PLIP interactions: 4 interactions with chain N, 3 interactions with chain Q Hydrophobic interactions: N:L.68, Q:I.79, Q:I.79, Q:E.81 Hydrogen bonds: N:P.69, N:L.71, N:Q.72 KTM.41: 9 residues within 4Å: Chain O: L.68, P.69, N.70, L.71, Q.72 Chain U: L.27, I.79, G.80, E.81 7 PLIP interactions: 3 interactions with chain U, 4 interactions with chain O Hydrophobic interactions: U:I.79, U:I.79, U:E.81, O:L.68 Hydrogen bonds: O:P.69, O:L.71, O:Q.72 KTM.45: 10 residues within 4Å: Chain D: L.27, L.77, I.79, G.80, E.81 Chain P: L.68, P.69, N.70, L.71, Q.72 7 PLIP interactions: 5 interactions with chain P, 2 interactions with chain D Hydrophobic interactions: P:L.68, P:L.68, D:I.79, D:I.79 Hydrogen bonds: P:P.69, P:L.71, P:Q.72 KTM.49: 11 residues within 4Å: Chain N: L.27, M.31, L.77, I.79, G.80, E.81 Chain Q: L.68, P.69, N.70, L.71, Q.72 7 PLIP interactions: 5 interactions with chain Q, 2 interactions with chain N Hydrophobic interactions: Q:L.68, Q:L.68, N:I.79, N:I.79 Hydrogen bonds: Q:P.69, Q:L.71, Q:Q.72 KTM.54: 10 residues within 4Å: Chain A: L.27, L.77, I.79, G.80, E.81 Chain S: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain S Hydrophobic interactions: A:I.79, A:I.79, A:E.81 Hydrogen bonds: S:P.69, S:L.71, S:Q.72 KTM.56: 10 residues within 4Å: Chain T: L.68, P.69, N.70, L.71, Q.72 Chain V: L.27, L.77, I.79, G.80, E.81 6 PLIP interactions: 4 interactions with chain T, 2 interactions with chain V Hydrophobic interactions: T:L.68, V:I.79, V:I.79 Hydrogen bonds: T:P.69, T:L.71, T:Q.72 KTM.58: 9 residues within 4Å: Chain O: L.27, I.79, G.80, E.81 Chain U: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 2 interactions with chain O, 4 interactions with chain U Hydrophobic interactions: O:I.79, O:I.79, U:L.68 Hydrogen bonds: U:P.69, U:L.71, U:Q.72 KTM.60: 10 residues within 4Å: Chain T: L.27, L.77, I.79, G.80, E.81 Chain V: L.68, P.69, N.70, L.71, Q.72 6 PLIP interactions: 2 interactions with chain T, 4 interactions with chain V Hydrophobic interactions: T:I.79, T:I.79, V:L.68 Hydrogen bonds: V:P.69, V:L.71, V:Q.72

26 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 6 residues within 4Å: Chain A: N.33, D.34, K.38 Chain J: D.132, T.136 Chain S: E.60 Ligand excluded by PLIP PG4.7: 5 residues within 4Å: Chain B: N.33, K.38 Chain C: D.132, T.136, Q.137 Ligand excluded by PLIP PG4.10: 5 residues within 4Å: Chain C: N.33, K.38 Chain G: D.132, T.136, Q.137 Ligand excluded by PLIP PG4.14: 5 residues within 4Å: Chain D: N.33, D.34, K.38 Chain T: D.132, T.136 Ligand excluded by PLIP PG4.15: 3 residues within 4Å: Chain D: K.6, Q.9, H.10 Ligand excluded by PLIP PG4.18: 8 residues within 4Å: Chain A: D.132, Y.133, T.136, Q.137 Chain E: N.33, D.34, G.36, K.38 Ligand excluded by PLIP PG4.20: 5 residues within 4Å: Chain D: D.132, T.136, Q.137 Chain F: N.33, K.38 Ligand excluded by PLIP PG4.21: 5 residues within 4Å: Chain F: D.132, T.136, Q.137 Chain I: N.33, K.38 Ligand excluded by PLIP PG4.23: 7 residues within 4Å: Chain G: N.33, G.36, K.38 Chain L: D.132, Y.133, T.136, Q.137 Ligand excluded by PLIP PG4.25: 6 residues within 4Å: Chain H: N.33, D.34, K.38 Chain U: D.132, Y.133, T.136 Ligand excluded by PLIP PG4.29: 7 residues within 4Å: Chain J: N.33, D.34, K.38 Chain K: D.132, Y.133, T.136, Q.137 Ligand excluded by PLIP PG4.30: 5 residues within 4Å: Chain E: D.132, T.136, Q.137 Chain K: N.33, K.38 Ligand excluded by PLIP PG4.32: 7 residues within 4Å: Chain B: D.132, Y.133, T.136, Q.137 Chain L: N.33, G.36, K.38 Ligand excluded by PLIP PG4.36: 6 residues within 4Å: Chain G: E.60 Chain M: N.33, D.34, K.38 Chain V: D.132, T.136 Ligand excluded by PLIP PG4.39: 5 residues within 4Å: Chain N: N.33, K.38 Chain O: D.132, T.136, Q.137 Ligand excluded by PLIP PG4.42: 5 residues within 4Å: Chain O: N.33, K.38 Chain S: D.132, T.136, Q.137 Ligand excluded by PLIP PG4.46: 5 residues within 4Å: Chain H: D.132, T.136 Chain P: N.33, D.34, K.38 Ligand excluded by PLIP PG4.47: 3 residues within 4Å: Chain P: K.6, Q.9, H.10 Ligand excluded by PLIP PG4.50: 8 residues within 4Å: Chain M: D.132, Y.133, T.136, Q.137 Chain Q: N.33, D.34, G.36, K.38 Ligand excluded by PLIP PG4.52: 5 residues within 4Å: Chain P: D.132, T.136, Q.137 Chain R: N.33, K.38 Ligand excluded by PLIP PG4.53: 5 residues within 4Å: Chain R: D.132, T.136, Q.137 Chain U: N.33, K.38 Ligand excluded by PLIP PG4.55: 7 residues within 4Å: Chain S: N.33, G.36, K.38 Chain X: D.132, Y.133, T.136, Q.137 Ligand excluded by PLIP PG4.57: 6 residues within 4Å: Chain I: D.132, Y.133, T.136 Chain T: N.33, D.34, K.38 Ligand excluded by PLIP PG4.61: 7 residues within 4Å: Chain V: N.33, D.34, K.38 Chain W: D.132, Y.133, T.136, Q.137 Ligand excluded by PLIP PG4.62: 5 residues within 4Å: Chain Q: D.132, T.136, Q.137 Chain W: N.33, K.38 Ligand excluded by PLIP PG4.64: 7 residues within 4Å: Chain N: D.132, Y.133, T.136, Q.137 Chain X: N.33, G.36, K.38 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Punchi Hewage, A.N.D. et al., Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity. J.Am.Chem.Soc. (2019)

Release Date

2019-05-08

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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