SMTL ID : 9o9y.1

Bacillus ytrEF vanadate trapped conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: F.31, I.33, V.44, S.64, G.65, S.66, G.67, K.68, S.69, T.70 Chain B: R.433 Chain D: H.158, H.161, N.164, E.165, L.166, S.167, Q.170 Ligands: VO4.2, MG.3 15 PLIP interactions: 10 interactions with chain A, 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:G.65, A:G.65, A:S.66, A:G.67, A:K.68, A:S.69, A:T.70, D:H.161, D:S.167, D:Q.170, D:Q.170, B:R.433 Salt bridges: A:K.68 pi-Stacking: A:F.31, A:F.31 ADP.6: 20 residues within 4Å: Chain A: H.158, H.161, N.164, E.165, L.166, S.167, Q.170 Chain C: R.433 Chain D: F.31, I.33, V.44, S.64, G.65, S.66, G.67, K.68, S.69, T.70 Ligands: VO4.7, MG.8 15 PLIP interactions: 4 interactions with chain A, 10 interactions with chain D, 1 interactions with chain C Hydrogen bonds: A:H.161, A:S.167, A:Q.170, A:Q.170, D:G.65, D:G.65, D:S.66, D:G.67, D:K.68, D:S.69, D:T.70, C:R.433 Salt bridges: D:K.68 pi-Stacking: D:F.31, D:F.31

2 x VO4: VANADATE ION(Non-covalent)

VO4.2: 14 residues within 4Å: Chain A: S.64, G.65, K.68, S.69, Q.114, E.191, H.224 Chain D: S.167, G.168, G.169, Q.170, S.195 Ligands: ADP.1, MG.3 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:G.65, A:K.68, A:Q.114, D:G.168, D:G.169, D:Q.170, D:S.195 VO4.7: 14 residues within 4Å: Chain A: S.167, G.168, G.169, Q.170, S.195 Chain D: S.64, G.65, K.68, S.69, Q.114, E.191, H.224 Ligands: ADP.6, MG.8 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:G.168, A:G.169, A:Q.170, D:G.65, D:K.68, D:Q.114, D:H.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: S.69, Q.114, D.190, E.191 Ligands: ADP.1, VO4.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.69 MG.8: 6 residues within 4Å: Chain D: S.69, Q.114, D.190, E.191 Ligands: ADP.6, VO4.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.69

2 x UNL: UNKNOWN LIGAND

UNL.4: 15 residues within 4Å: Chain B: L.38, S.39, V.41, G.42, F.43, I.45, Q.46, L.297, V.300, G.301 Chain C: F.293, G.296, L.297, V.300 Ligands: UNL.5 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:F.293, C:L.297, C:V.300, B:L.38, B:L.38, B:F.43, B:F.43, B:F.43, B:I.45, B:Q.46 UNL.5: 15 residues within 4Å: Chain B: F.293, G.296, L.297, V.300 Chain C: L.38, S.39, V.41, G.42, F.43, I.45, Q.46, L.297, V.300, G.301 Ligands: UNL.4 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.38, C:L.38, C:V.41, C:F.43, C:I.45, C:Q.46, C:L.297, C:V.300, B:F.293, B:L.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, P. et al., Structural Analysis of a Mechanotransmission ABC Transporter Induced By Cell Wall Targeting Antibiotics. To Be Published

Release Date

2025-10-15

Peptides

ABC transporter ATP-binding protein YtrE: AD
ABC transporter permease YtrF: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

B
D

C
C

Membrane

We predict this structure to be a membrane protein.
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ABC transporter ATP-binding protein YtrE

ABC transporter permease YtrF

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