SMTL ID : 8h5a.3 (7 other biounits)

Crystal structure of YhaJ effector binding domain (ligand-bound)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

6 x 7DV: 2-methylbenzene-1,4-diol(Non-covalent)

7DV.1: 7 residues within 4Å: Chain A: E.13, L.15, L.43, V.123, I.137, K.140, T.152 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.15, A:L.15, A:L.15, A:V.123, A:I.137 Hydrogen bonds: A:E.13, A:K.140, A:T.152 7DV.2: 7 residues within 4Å: Chain A: A.14, L.15, V.16, P.17, P.156, M.157 Ligands: 7DV.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.17, A:M.157 Hydrogen bonds: A:M.157 7DV.3: 4 residues within 4Å: Chain A: P.17, P.19, A.20 Ligands: 7DV.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.17, A:P.19 7DV.5: 5 residues within 4Å: Chain B: E.13, L.15, L.43, V.111, K.140 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.15, B:L.43, B:V.111 Hydrogen bonds: B:E.13, B:L.43 7DV.6: 5 residues within 4Å: Chain B: L.15, P.17, P.156, M.157 Ligands: 7DV.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.156, B:M.157 7DV.7: 4 residues within 4Å: Chain B: P.17, P.19, A.20 Ligands: 7DV.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.17

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: T.12, E.13, A.14, V.16, T.18, T.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.12, A:T.12, A:T.18 NA.8: 5 residues within 4Å: Chain A: D.139 Chain B: T.12, V.16, T.18, T.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.16, B:T.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M. et al., Structural basis of transcription factor YhaJ for DNT detection. Iscience (2023)

Release Date

2023-10-25

Peptides

HTH-type transcriptional regulator YhaJ: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

HTH-type transcriptional regulator YhaJ

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