SMTL ID : 8dck.1

Structure of hemolysin A secretion system HlyB/D complex, ATP-bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: Y.477, I.484, R.503, S.504, G.505, S.506, G.507, K.508, S.509, T.510, Q.550, Q.631, H.662 Chain B: G.605, L.606, S.607, G.608, G.609, Q.610, A.635 Ligands: MG.2 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.505, A:G.505, A:S.506, A:G.507, A:K.508, A:S.509, A:S.509, A:T.510, A:Q.550, A:Q.631, A:Q.631, B:G.605, B:S.607, B:G.608, B:G.609, B:Q.610 Salt bridges: A:K.508, A:K.508, A:H.662 pi-Stacking: A:Y.477, A:Y.477 ATP.3: 20 residues within 4Å: Chain A: A.604, G.605, S.607, G.608, G.609, Q.610 Chain B: Y.477, K.478, I.484, R.503, S.504, G.505, S.506, G.507, K.508, S.509, T.510, Q.550, H.662 Ligands: MG.4 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:S.607, A:G.608, A:G.609, A:Q.610, A:Q.610, B:K.478, B:G.505, B:G.505, B:G.507, B:K.508, B:S.509, B:S.509, B:S.509, B:T.510 Salt bridges: B:H.662 ATP.5: 21 residues within 4Å: Chain E: Y.477, I.484, R.503, S.504, G.505, S.506, G.507, K.508, S.509, T.510, Q.550, Q.631, H.662 Chain F: G.605, L.606, S.607, G.608, G.609, Q.610, A.635 Ligands: MG.6 21 PLIP interactions: 16 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:G.505, E:G.505, E:S.506, E:G.507, E:K.508, E:S.509, E:S.509, E:T.510, E:Q.550, E:Q.631, E:Q.631, F:G.605, F:S.607, F:G.608, F:G.609, F:Q.610 Salt bridges: E:K.508, E:K.508, E:H.662 pi-Stacking: E:Y.477, E:Y.477 ATP.7: 20 residues within 4Å: Chain E: A.604, G.605, S.607, G.608, G.609, Q.610 Chain F: Y.477, K.478, I.484, R.503, S.504, G.505, S.506, G.507, K.508, S.509, T.510, Q.550, H.662 Ligands: MG.8 15 PLIP interactions: 10 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:K.478, F:G.505, F:G.505, F:G.507, F:K.508, F:S.509, F:S.509, F:S.509, F:T.510, E:S.607, E:G.608, E:G.609, E:Q.610, E:Q.610 Salt bridges: F:H.662 ATP.9: 21 residues within 4Å: Chain I: Y.477, I.484, R.503, S.504, G.505, S.506, G.507, K.508, S.509, T.510, Q.550, Q.631, H.662 Chain J: G.605, L.606, S.607, G.608, G.609, Q.610, A.635 Ligands: MG.10 21 PLIP interactions: 16 interactions with chain I, 5 interactions with chain J Hydrogen bonds: I:G.505, I:G.505, I:S.506, I:G.507, I:K.508, I:S.509, I:S.509, I:T.510, I:Q.550, I:Q.631, I:Q.631, J:G.605, J:S.607, J:G.608, J:G.609, J:Q.610 Salt bridges: I:K.508, I:K.508, I:H.662 pi-Stacking: I:Y.477, I:Y.477 ATP.11: 20 residues within 4Å: Chain I: A.604, G.605, S.607, G.608, G.609, Q.610 Chain J: Y.477, K.478, I.484, R.503, S.504, G.505, S.506, G.507, K.508, S.509, T.510, Q.550, H.662 Ligands: MG.12 15 PLIP interactions: 10 interactions with chain J, 5 interactions with chain I Hydrogen bonds: J:K.478, J:G.505, J:G.505, J:G.507, J:K.508, J:S.509, J:S.509, J:S.509, J:T.510, I:S.607, I:G.608, I:G.609, I:Q.610, I:Q.610 Salt bridges: J:H.662

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.509, Q.550, Q.631 Chain B: S.607 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.509 MG.4: 3 residues within 4Å: Chain B: S.509, Q.550 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.509 MG.6: 5 residues within 4Å: Chain E: S.509, Q.550, Q.631 Chain F: S.607 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.509 MG.8: 3 residues within 4Å: Chain F: S.509, Q.550 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.509 MG.10: 5 residues within 4Å: Chain I: S.509, Q.550, Q.631 Chain J: S.607 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.509 MG.12: 3 residues within 4Å: Chain J: S.509, Q.550 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.509

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, H. et al., The hemolysin A secretion system is a multi-engine pump containing three ABC transporters. Cell (2022)

Release Date

2022-09-14

Peptides

Alpha-hemolysin translocation ATP-binding protein HlyB: ABEFIJ
Membrane fusion protein (MFP) family protein: CDGHKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
I

F
J

I
E

J
F

C
C

D
D

G
K

H
L

K
G

L
H

Membrane

We predict this structure to be a membrane protein.
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Alpha-hemolysin translocation ATP-binding protein HlyB

Membrane fusion protein (MFP) family protein