SMTL ID : 5ejl.2 (1 other biounit)

MrkH, A novel c-di-GMP dependence transcription regulatory factor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.1: 18 residues within 4Å: Chain A: R.126, R.127, R.128, R.131, D.158, I.159, S.160, G.162, G.163, C.164, A.165, K.202, S.223, C.224, Q.225 Ligands: C2E.2, SO4.3, EDO.7 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.126, A:R.127, A:R.128, A:R.131, A:S.160, A:S.160 Water bridges: A:R.128, A:R.128, A:D.129, A:D.129, A:R.131, A:R.131 Salt bridges: A:R.128, A:R.131, A:D.158, A:K.202 pi-Cation interactions: A:R.126, A:R.131 C2E.2: 15 residues within 4Å: Chain A: L.85, H.87, G.91, K.92, V.124, Q.125, R.126, R.127, R.131, K.202, N.203, I.205, Q.221, S.223 Ligands: C2E.1 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Q.125, A:Q.125, A:R.126, A:R.126, A:R.127, A:R.127, A:R.131, A:R.131, A:N.203, A:Q.221, A:S.223 Water bridges: A:S.19, A:H.87, A:H.87, A:K.202, A:K.202, A:N.203 Salt bridges: A:H.87, A:R.127, A:K.157 pi-Cation interactions: A:R.127 C2E.9: 18 residues within 4Å: Chain B: R.126, R.127, R.128, R.131, D.158, I.159, S.160, G.162, G.163, C.164, A.165, K.202, S.223, C.224, Q.225 Ligands: C2E.10, SO4.11, EDO.15 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.126, B:R.127, B:R.128, B:R.131, B:S.160, B:S.160 Water bridges: B:R.128, B:R.128, B:D.129, B:D.129, B:R.131, B:R.131 Salt bridges: B:R.128, B:R.131, B:D.158, B:K.202 pi-Cation interactions: B:R.126, B:R.131 C2E.10: 15 residues within 4Å: Chain B: L.85, H.87, G.91, K.92, V.124, Q.125, R.126, R.127, R.131, K.202, N.203, I.205, Q.221, S.223 Ligands: C2E.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.125, B:Q.125, B:R.126, B:R.126, B:R.127, B:R.127, B:R.131, B:R.131, B:N.203, B:Q.221, B:S.223 Water bridges: B:S.19, B:E.46, B:E.46, B:K.202, B:K.202, B:N.203 Salt bridges: B:H.87, B:R.127, B:K.157 pi-Cation interactions: B:R.127

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

SO4.3: 4 residues within 4Å: Chain A: H.178, N.179, K.202 Ligands: C2E.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179 Water bridges: A:K.202 Salt bridges: A:H.178, A:K.202 SO4.4: 4 residues within 4Å: Chain A: R.17, G.18, S.19, H.20 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.18, A:H.20 Water bridges: A:H.20, B:E.32 Salt bridges: A:R.17, A:H.20 SO4.5: 8 residues within 4Å: Chain A: H.20, T.22, T.25, K.27 Chain B: H.20, T.25, K.27 Ligands: SO4.13 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.25, B:T.25 Water bridges: A:K.27, A:K.27, B:K.27, B:K.27 Salt bridges: A:H.20, A:K.27, B:H.20, B:K.27 SO4.11: 4 residues within 4Å: Chain B: H.178, N.179, K.202 Ligands: C2E.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.179 Water bridges: B:K.202 Salt bridges: B:H.178, B:K.202 SO4.12: 4 residues within 4Å: Chain B: R.17, G.18, S.19, H.20 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.18, B:H.20 Water bridges: B:S.19 Salt bridges: B:R.17, B:H.20 SO4.13: 8 residues within 4Å: Chain A: H.20, T.25, K.27 Chain B: H.20, T.22, T.25, K.27 Ligands: SO4.5 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.25, A:T.25 Water bridges: A:K.27, A:K.27, B:K.27, B:K.27 Salt bridges: A:H.20, A:K.27, B:H.20, B:K.27

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 3 residues within 4Å: Chain A: E.94, C.120, Q.122 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.96 EDO.7: 3 residues within 4Å: Chain A: K.92, R.126 Ligands: C2E.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.92, A:K.92, A:R.126 Water bridges: A:R.126 EDO.8: 1 residues within 4Å: Chain A: N.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.148 EDO.14: 3 residues within 4Å: Chain B: E.94, C.120, Q.122 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.96 EDO.15: 3 residues within 4Å: Chain B: K.92, R.126 Ligands: C2E.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.92, B:K.92, B:R.126 Water bridges: B:R.126 EDO.16: 1 residues within 4Å: Chain B: N.148 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., The PilZ domain of MrkH represents a novel DNA binding motif. Protein Cell (2016)

Release Date

2016-10-19

Peptides

Klebsiella pneumoniae genome assembly NOVST: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Klebsiella pneumoniae genome assembly NOVST

Related Entries With Identical Sequence