SMTL ID : 5jm8.3 (2 other biounits)

The structure of ATP-bound aerobactin synthetase IucA from a hypervirulent pathotype of Klebsiella pneumoniae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: L.145, G.148, H.149, S.264, R.266, S.267, K.278, L.285, T.286, R.290, R.349, V.365, H.427, Q.428, Q.429, N.430, R.446, D.447, Q.449, N.489 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.264, A:S.267, A:T.286, A:R.290, A:R.290, A:Q.428, A:R.446, A:D.447, A:N.489, A:N.489 Water bridges: A:A.150, A:A.150, A:R.349, A:R.349 Salt bridges: A:R.266, A:K.278, A:K.278, A:R.290, A:R.290, A:R.349, A:H.427 pi-Stacking: A:H.149 ATP.3: 19 residues within 4Å: Chain B: L.145, G.148, H.149, S.264, R.266, S.267, K.278, T.286, R.290, R.349, V.365, H.427, Q.428, Q.429, N.430, D.447, Q.449, N.489 Ligands: MG.4 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:A.150, B:S.264, B:R.266, B:S.267, B:T.286, B:R.290, B:Q.428, B:Q.429, B:Q.449, B:N.489, B:N.489 Water bridges: B:H.149, B:T.263 Salt bridges: B:R.266, B:K.278, B:K.278, B:R.290, B:R.290, B:R.349, B:H.427, B:R.446 pi-Stacking: B:H.149 ATP.5: 21 residues within 4Å: Chain C: L.145, G.148, H.149, S.264, R.266, S.267, K.278, L.285, T.286, R.290, R.349, V.365, H.427, Q.428, Q.429, N.430, R.446, D.447, Q.449, N.489 Ligands: MG.6 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:S.264, C:R.266, C:S.267, C:T.286, C:R.290, C:Q.428, C:D.447, C:N.489, C:N.489 Water bridges: C:A.150, C:A.150, C:S.264, C:S.264, C:R.290, C:R.349 Salt bridges: C:R.266, C:K.278, C:K.278, C:R.290, C:R.290, C:R.349, C:H.427 ATP.7: 19 residues within 4Å: Chain D: L.145, G.148, H.149, S.264, R.266, S.267, K.278, L.285, T.286, R.290, R.349, V.365, H.427, Q.428, Q.429, N.430, D.447, N.489 Ligands: MG.8 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:S.264, D:S.267, D:T.286, D:R.290, D:Q.428, D:Q.429, D:D.447, D:N.489, D:N.489 Water bridges: D:A.150, D:A.150, D:S.264, D:T.286, D:R.290, D:R.349 Salt bridges: D:R.266, D:K.278, D:K.278, D:R.290, D:R.290, D:R.349, D:H.427 pi-Stacking: D:H.149 ATP.9: 20 residues within 4Å: Chain E: L.145, G.148, H.149, S.264, R.266, S.267, K.278, L.285, T.286, R.290, R.349, V.365, H.427, Q.428, Q.429, N.430, D.447, Q.449, N.489 Ligands: MG.10 22 PLIP interactions: 22 interactions with chain E Hydrogen bonds: E:S.264, E:R.266, E:S.267, E:T.286, E:T.286, E:R.290, E:Q.429, E:Q.449, E:N.489, E:N.489 Water bridges: E:A.150, E:A.150, E:R.349, E:R.349 Salt bridges: E:R.266, E:K.278, E:K.278, E:R.290, E:R.290, E:R.349, E:H.427 pi-Stacking: E:H.149 ATP.11: 19 residues within 4Å: Chain F: L.145, G.148, H.149, S.264, R.266, S.267, K.278, L.285, T.286, R.290, R.349, V.365, H.427, Q.429, N.430, D.447, Q.449, N.489 Ligands: MG.12 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:S.264, F:R.266, F:S.267, F:T.286, F:R.290, F:Q.429, F:D.447, F:Q.449, F:N.489, F:N.489 Water bridges: F:H.149, F:R.290, F:R.290 Salt bridges: F:R.266, F:K.278, F:K.278, F:R.290, F:R.290, F:R.349, F:H.427 ATP.13: 19 residues within 4Å: Chain G: L.145, G.148, H.149, S.264, R.266, S.267, K.278, L.285, T.286, R.290, R.349, V.365, H.427, Q.428, Q.429, N.430, D.447, N.489 Ligands: MG.14 25 PLIP interactions: 25 interactions with chain G Hydrogen bonds: G:S.264, G:R.266, G:S.267, G:T.286, G:T.286, G:Q.429, G:R.446, G:N.489, G:N.489 Water bridges: G:A.150, G:A.150, G:T.262, G:T.286, G:R.290, G:R.349, G:R.349, G:R.446 Salt bridges: G:R.266, G:K.278, G:K.278, G:R.290, G:R.290, G:R.349, G:H.427 pi-Stacking: G:H.149 ATP.15: 20 residues within 4Å: Chain H: L.145, G.148, H.149, S.264, R.266, S.267, K.278, T.286, R.290, R.349, V.365, H.427, Q.428, Q.429, N.430, R.446, D.447, Q.449, N.489 Ligands: MG.16 22 PLIP interactions: 22 interactions with chain H Hydrogen bonds: H:S.264, H:S.267, H:T.286, H:T.286, H:Q.429, H:R.446, H:D.447, H:Q.449, H:N.489, H:N.489 Water bridges: H:A.150, H:T.262, H:R.290, H:R.349 Salt bridges: H:R.266, H:K.278, H:K.278, H:R.290, H:R.290, H:R.349, H:H.427 pi-Stacking: H:H.149

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.429, N.430, D.447 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.447 MG.4: 4 residues within 4Å: Chain B: Q.429, N.430, D.447 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.447 MG.6: 4 residues within 4Å: Chain C: Q.429, N.430, D.447 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.447 MG.8: 5 residues within 4Å: Chain D: H.427, Q.429, N.430, D.447 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.447 MG.10: 4 residues within 4Å: Chain E: Q.429, N.430, D.447 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain F: Q.429, N.430, D.447 Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain G: H.427, Q.429, N.430, D.447 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.447 MG.16: 5 residues within 4Å: Chain H: H.427, Q.429, N.430, D.447 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.447

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bailey, D.C. et al., Structural and Functional Characterization of Aerobactin Synthetase IucA from a Hypervirulent Pathotype of Klebsiella pneumoniae. Biochemistry (2016)

Release Date

2016-06-15

Peptides

Aerobactin synthase IucA: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Aerobactin synthase IucA

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