SMTL ID : 4xrf.1

Crystal structure of MepR like protein complexed with pseudoligands

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-tetramer

Ligands

16 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: D.85, R.87, V.88 Ligand excluded by PLIP PO4.2: 9 residues within 4Å: Chain A: Y.37, K.40 Chain D: M.1, T.2, H.3, I.4, D.5, K.6 Ligands: GOL.6 Ligand excluded by PLIP PO4.3: 1 residues within 4Å: Chain A: R.49 Ligand excluded by PLIP PO4.8: 6 residues within 4Å: Chain A: K.96, R.100 Chain C: L.76, K.96, R.100 Ligands: PO4.28 Ligand excluded by PLIP PO4.11: 3 residues within 4Å: Chain B: D.85, R.87, V.88 Ligand excluded by PLIP PO4.12: 9 residues within 4Å: Chain B: Y.37, K.40 Chain C: M.1, T.2, H.3, I.4, D.5, K.6 Ligands: GOL.16 Ligand excluded by PLIP PO4.13: 1 residues within 4Å: Chain B: R.49 Ligand excluded by PLIP PO4.18: 6 residues within 4Å: Chain B: K.96, R.100 Chain D: L.76, K.96, R.100 Ligands: PO4.38 Ligand excluded by PLIP PO4.21: 3 residues within 4Å: Chain C: D.85, R.87, V.88 Ligand excluded by PLIP PO4.22: 9 residues within 4Å: Chain B: M.1, T.2, H.3, I.4, D.5, K.6 Chain C: Y.37, K.40 Ligands: GOL.26 Ligand excluded by PLIP PO4.23: 1 residues within 4Å: Chain C: R.49 Ligand excluded by PLIP PO4.28: 6 residues within 4Å: Chain A: L.76, K.96, R.100 Chain C: K.96, R.100 Ligands: PO4.8 Ligand excluded by PLIP PO4.31: 3 residues within 4Å: Chain D: D.85, R.87, V.88 Ligand excluded by PLIP PO4.32: 9 residues within 4Å: Chain A: M.1, T.2, H.3, I.4, D.5, K.6 Chain D: Y.37, K.40 Ligands: GOL.36 Ligand excluded by PLIP PO4.33: 1 residues within 4Å: Chain D: R.49 Ligand excluded by PLIP PO4.38: 6 residues within 4Å: Chain B: L.76, K.96, R.100 Chain D: K.96, R.100 Ligands: PO4.18 Ligand excluded by PLIP

4 x ISQ: ISOQUINOLINE(Non-covalent)

ISQ.4: 12 residues within 4Å: Chain A: Q.8, A.11, F.131, L.134 Chain D: A.11, I.14, G.15, M.18, F.116, F.131 Ligands: DAO.5, ISQ.34 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:I.14, D:F.116, D:F.131, A:A.11, A:F.131, A:F.131, A:L.134 Hydrogen bonds: A:Q.8 ISQ.14: 12 residues within 4Å: Chain B: Q.8, A.11, F.131, L.134 Chain C: A.11, I.14, G.15, M.18, F.116, F.131 Ligands: DAO.15, ISQ.24 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.14, C:F.116, C:F.131, B:A.11, B:F.131, B:F.131, B:L.134 Hydrogen bonds: B:Q.8 ISQ.24: 12 residues within 4Å: Chain B: A.11, I.14, G.15, M.18, F.116, F.131 Chain C: Q.8, A.11, F.131, L.134 Ligands: ISQ.14, DAO.25 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:I.14, B:F.116, B:F.131, C:A.11, C:F.131, C:F.131, C:L.134 Hydrogen bonds: C:Q.8 ISQ.34: 12 residues within 4Å: Chain A: A.11, I.14, G.15, M.18, F.116, F.131 Chain D: Q.8, A.11, F.131, L.134 Ligands: ISQ.4, DAO.35 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:I.14, A:F.116, A:F.131, D:A.11, D:F.131, D:F.131, D:L.134 Hydrogen bonds: D:Q.8

4 x DAO: LAURIC ACID(Non-covalent)

DAO.5: 9 residues within 4Å: Chain A: F.12, K.16, Q.19 Chain B: T.20, L.23 Chain D: Q.19 Ligands: ISQ.4, DAO.15, DAO.35 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.23, A:F.12, A:K.16 Salt bridges: A:K.16 DAO.15: 9 residues within 4Å: Chain A: T.20, L.23 Chain B: F.12, K.16, Q.19 Chain C: Q.19 Ligands: DAO.5, ISQ.14, DAO.25 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.12, B:K.16, A:L.23 Salt bridges: B:K.16 DAO.25: 9 residues within 4Å: Chain B: Q.19 Chain C: F.12, K.16, Q.19 Chain D: T.20, L.23 Ligands: DAO.15, ISQ.24, DAO.35 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.12, C:K.16, D:L.23 Water bridges: C:T.20, C:T.20, D:T.20, D:T.20 Salt bridges: C:K.16 DAO.35: 9 residues within 4Å: Chain A: Q.19 Chain C: T.20, L.23 Chain D: F.12, K.16, Q.19 Ligands: DAO.5, DAO.25, ISQ.34 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.12, D:K.16, C:L.23 Water bridges: D:T.20, D:T.20, C:T.20, C:T.20 Salt bridges: D:K.16

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: Y.37, K.40, I.41, H.44, Y.45 Ligands: PO4.2, SO4.10 No protein-ligand interaction detected (PLIP) GOL.7: 1 residues within 4Å: Chain A: R.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.79 GOL.16: 7 residues within 4Å: Chain B: Y.37, K.40, I.41, H.44, Y.45 Ligands: PO4.12, SO4.20 No protein-ligand interaction detected (PLIP) GOL.17: 1 residues within 4Å: Chain B: R.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.79 GOL.26: 7 residues within 4Å: Chain C: Y.37, K.40, I.41, H.44, Y.45 Ligands: PO4.22, SO4.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.44 GOL.27: 1 residues within 4Å: Chain C: R.79 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.79 Water bridges: C:R.79 GOL.36: 7 residues within 4Å: Chain D: Y.37, K.40, I.41, H.44, Y.45 Ligands: PO4.32, SO4.40 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.44 GOL.37: 1 residues within 4Å: Chain D: R.79 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.79 Water bridges: D:R.79

4 x NI: NICKEL (II) ION(Non-covalent)

NI.9: 2 residues within 4Å: Chain A: H.81, R.86 No protein-ligand interaction detected (PLIP) NI.19: 2 residues within 4Å: Chain B: H.81, R.86 No protein-ligand interaction detected (PLIP) NI.29: 2 residues within 4Å: Chain C: H.81, R.86 No protein-ligand interaction detected (PLIP) NI.39: 2 residues within 4Å: Chain D: H.81, R.86 No protein-ligand interaction detected (PLIP)

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

SO4.10: 5 residues within 4Å: Chain A: Y.37, Y.45, K.56 Chain D: K.6 Ligands: GOL.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.37 Salt bridges: A:K.56, D:K.6 SO4.20: 5 residues within 4Å: Chain B: Y.37, Y.45, K.56 Chain C: K.6 Ligands: GOL.16 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:K.6, B:K.56 Hydrogen bonds: B:Y.37 SO4.30: 5 residues within 4Å: Chain B: K.6 Chain C: Y.37, Y.45, K.56 Ligands: GOL.26 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.45 Salt bridges: C:K.56, B:K.6 SO4.40: 5 residues within 4Å: Chain A: K.6 Chain D: Y.37, Y.45, K.56 Ligands: GOL.36 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.45 Salt bridges: D:K.56, A:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, M. et al., Crystal structure of MepR like protein complexed with pseudoligands. to be published

Release Date

2016-02-10

Peptides

Transcriptional regulator, MarR family: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Transcriptional regulator, MarR family