SMTL ID : 8sbh.1

YeiE effector binding domain from E. coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 10 residues within 4Å: Chain A: S.7, S.8, T.9, N.37, S.38, E.56, R.102, S.106, G.107, T.108 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.8, A:S.8, A:T.9, A:S.38, A:E.56, A:S.106, A:S.106, A:G.107, A:T.108 Salt bridges: A:R.102 SO4.11: 7 residues within 4Å: Chain A: K.136, D.155, Q.156 Chain B: Y.13, K.136, D.155, Q.156 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.156, A:D.155, A:Q.156 Water bridges: B:K.136, B:K.136, B:K.136, B:R.140, B:R.140, B:V.152, B:D.155, B:D.155, A:K.136 Salt bridges: B:K.136, A:K.136 SO4.12: 9 residues within 4Å: Chain B: S.7, S.8, N.37, S.38, E.56, R.102, S.106, G.107, T.108 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.37, B:S.38, B:S.38, B:S.38, B:G.107, B:T.108, B:T.108 Water bridges: B:S.8, B:Q.39, B:R.102 Salt bridges: B:R.102

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: N.12, N.131, E.133 Chain B: S.8, N.12, N.131, S.132, E.133 Ligands: GOL.8 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.8, B:N.12, B:S.132, A:N.12, A:E.133, A:E.133 Water bridges: B:E.133, B:E.133, A:S.132 GOL.3: 8 residues within 4Å: Chain A: E.32, L.33, S.34 Chain B: E.103, E.128, L.129, G.130 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.34 Water bridges: A:L.33, A:L.33, A:V.35 GOL.4: 11 residues within 4Å: Chain A: A.78, A.79, S.82, P.83, L.84, A.97, P.98, G.142, L.143, G.144, I.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.142 GOL.5: 8 residues within 4Å: Chain A: M.1, R.23, P.30, I.31 Chain B: M.125, A.126, M.127, E.128 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.31, A:I.31 Water bridges: A:I.31, A:I.31, B:A.126, B:E.128 GOL.6: 2 residues within 4Å: Chain A: S.118, H.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.118 GOL.7: 4 residues within 4Å: Chain A: A.17, A.20, R.21 Chain B: H.141 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.141, A:A.17 Water bridges: B:H.141 GOL.8: 11 residues within 4Å: Chain A: S.8, N.12, V.35, G.36, N.37, R.102, E.103, G.130, N.131 Chain B: N.131 Ligands: GOL.2 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:N.131 Hydrogen bonds: A:N.12, A:R.102 GOL.9: 5 residues within 4Å: Chain A: P.68, W.69, L.70, E.71, T.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.71, A:T.175 GOL.10: 7 residues within 4Å: Chain A: R.3, Y.5, E.32, S.34, R.49, V.50 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.49, A:R.49 Water bridges: A:I.4, A:Y.5, A:E.32 GOL.13: 8 residues within 4Å: Chain A: E.103, R.104, E.128, L.129, G.130 Chain B: E.32, L.33, S.34 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.34, A:E.128, A:E.128 Water bridges: B:L.33, B:S.34, A:G.130

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 3 residues within 4Å: Chain B: P.58, T.175, W.177 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Momany, C. et al., FinR, a LysR-type transcriptional regulator involved in sulfur homeostasis with homologs in diverse microorganisms. To Be Published

Release Date

2024-04-17

Peptides

Transcriptional regulator YeiE, LysR family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transcriptional regulator YeiE, LysR family