SMTL ID : 7w78.1

Heme exporter HrtBA in complex with Mg-AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.50, Q.90 Ligands: ANP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.50, H2O.1, H2O.1 MG.9: 3 residues within 4Å: Chain C: S.50, Q.90 Ligands: ANP.10 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.50, H2O.5, H2O.6

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 23 residues within 4Å: Chain A: Y.16, V.23, A.25, E.44, S.45, G.46, S.47, G.48, K.49, S.50, T.51, Q.90, E.165, H.198 Chain C: R.135, A.138, Q.139, S.141, G.142, G.143, Q.144, A.169 Ligands: MG.1 23 PLIP interactions: 10 interactions with chain C, 13 interactions with chain A Hydrogen bonds: C:R.135, C:R.135, C:A.138, C:S.141, C:G.142, C:G.143, C:Q.144, C:Q.144, C:Q.144, C:A.169, A:G.46, A:G.46, A:S.47, A:G.48, A:K.49, A:K.49, A:K.49, A:S.50, A:S.50, A:T.51, A:Q.90 Water bridges: A:S.50, A:Q.90 ANP.10: 23 residues within 4Å: Chain A: R.135, A.138, Q.139, S.141, G.142, G.143, Q.144, A.169 Chain C: Y.16, V.23, A.25, E.44, S.45, G.46, S.47, G.48, K.49, S.50, T.51, Q.90, E.165, H.198 Ligands: MG.9 25 PLIP interactions: 15 interactions with chain C, 10 interactions with chain A Hydrogen bonds: C:G.46, C:G.46, C:S.47, C:G.48, C:K.49, C:K.49, C:K.49, C:S.50, C:S.50, C:T.51, C:T.51, C:Q.90, A:R.135, A:R.135, A:A.138, A:S.141, A:G.142, A:G.143, A:Q.144, A:Q.144, A:Q.144, A:A.169 Water bridges: C:Y.16, C:S.50, C:Q.90

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: P.92, N.93, L.94, R.145 Chain C: Q.91 Chain D: A.344 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.91, A:N.93, A:L.94 ACT.4: 4 residues within 4Å: Chain A: R.119, L.154, G.156, N.157 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.154 Hydrogen bonds: A:L.154, A:N.157 Water bridges: A:R.119 Salt bridges: A:R.119 ACT.11: 6 residues within 4Å: Chain A: Q.91 Chain B: A.344 Chain C: P.92, N.93, L.94, R.145 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.93, C:L.94, A:Q.91 ACT.12: 4 residues within 4Å: Chain C: R.119, L.154, G.156, N.157 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.154 Hydrogen bonds: C:L.154, C:N.157 Water bridges: C:R.119 Salt bridges: C:R.119

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain B: Q.37, S.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.37, B:S.308 GOL.13: 2 residues within 4Å: Chain D: Q.37, S.308 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.37, D:S.308

4 x MYZ: Myristoleic acid(Non-covalent)

MYZ.6: 4 residues within 4Å: Chain B: G.13, S.20, L.24, L.284 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.24, B:L.284 MYZ.7: 5 residues within 4Å: Chain B: G.13, R.14, L.17 Chain D: V.239, I.326 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.239, D:I.326, D:I.326, B:R.14 MYZ.14: 4 residues within 4Å: Chain D: G.13, S.20, L.24, L.284 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.24, D:L.284 MYZ.15: 5 residues within 4Å: Chain B: V.239, I.326 Chain D: G.13, R.14, L.17 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.239, B:I.326, B:I.326, D:R.14

2 x D12: DODECANE(Non-covalent)

D12.8: 3 residues within 4Å: Chain B: I.5, R.6, I.276 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.5, B:I.5, B:I.276 D12.16: 3 residues within 4Å: Chain D: I.5, R.6, I.276 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.5, D:I.5, D:I.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, H. et al., Structural basis for heme detoxification by an ATP-binding cassette-type efflux pump in gram-positive pathogenic bacteria. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-06-22

Peptides

Putative ABC transport system, ATP-binding protein: AC
Putative ABC transport system integral membrane protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Membrane

We predict this structure to be a membrane protein.
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Putative ABC transport system, ATP-binding protein

Putative ABC transport system integral membrane protein

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