SMTL ID : 7ubj.1

Transcription antitermination factor Qlambda, type-I crystal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.58, D.60, C.61, G.65, C.84, R.86, C.87, G.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.58, A:C.61, A:C.84, A:C.87 ZN.9: 8 residues within 4Å: Chain B: C.58, D.60, C.61, G.65, C.84, R.86, C.87, G.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.58, B:C.61, B:C.84, B:C.87

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

CL.2: 5 residues within 4Å: Chain A: A.97, S.98, Q.113, W.116, K.121 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: R.78 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: R.66, R.78, V.80, E.81 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: A.6, Y.9, E.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.9, A:E.134 GOL.13: 3 residues within 4Å: Chain B: A.6, Y.9, E.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.9, B:E.134 Water bridges: B:Y.9, B:E.134

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

EDO.4: 5 residues within 4Å: Chain A: R.59, D.60, H.62 Chain B: S.98 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.62 EDO.5: 6 residues within 4Å: Chain A: H.62, D.139 Chain B: S.98, Y.101, R.102 Ligands: EDO.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.102, B:R.102 Water bridges: A:N.143 EDO.6: 4 residues within 4Å: Chain A: K.34, Q.37, V.38, T.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.37 Water bridges: A:T.41 EDO.14: 8 residues within 4Å: Chain B: S.50, A.51, A.52, T.53, P.54, G.55, A.56, R.57 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.50, B:T.53, B:G.55 Water bridges: B:R.57 EDO.15: 1 residues within 4Å: Chain B: A.52 2 PLIP interactions: 2 interactions with chain B Water bridges: B:C.48, B:A.51

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 7 residues within 4Å: Chain A: L.27, T.31, L.107, I.108, P.109, N.110, L.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.107 Water bridges: A:T.31 PEG.8: 4 residues within 4Å: Chain A: A.45, D.46, R.49, P.96 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.46 PEG.16: 1 residues within 4Å: Chain B: R.118 No protein-ligand interaction detected (PLIP)

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

PO4.10: 5 residues within 4Å: Chain B: G.55, R.57, C.58, R.59, R.86 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.59 Water bridges: B:R.57, B:C.58, B:R.59, B:R.86 Salt bridges: B:R.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., In transcription antitermination by Q lambda , NusA induces refolding of Q lambda to form a nozzle that extends the RNA polymerase RNA-exit channel. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-09-28

Peptides

Antitermination protein Q: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Antitermination protein Q

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