SMTL ID : 1wmq.1

Structure of the HutP antitermination complex bound to a single stranded region of hut mRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

6 x U- U- U- A- G- U- U: 5'-R(P*UP*UP*UP*AP*GP*UP*U)-3'(Non-covalent)

U-U-U-A-G-U-U.1: 25 residues within 4Å: Chain A: K.40, V.41, G.42, S.43, M.44, A.52, T.55, A.56, K.59, L.96, T.98, V.99, G.100, L.101, T.127, A.130, P.131, I.132, K.133, E.136 Chain E: A.51, E.54, T.55 Ligands: U-U-U-A-G-U-U.7, U-U-U-A-G-U-U.13 Protein-ligand interaction information (PLIP) not available U-U-U-A-G-U-U.2: 25 residues within 4Å: Chain B: K.40, V.41, G.42, S.43, M.44, A.52, T.55, A.56, K.59, L.96, T.98, V.99, G.100, L.101, T.127, A.130, P.131, I.132, K.133, E.136 Chain D: A.51, E.54, T.55 Ligands: U-U-U-A-G-U-U.8, U-U-U-A-G-U-U.14 Protein-ligand interaction information (PLIP) not available U-U-U-A-G-U-U.7: 25 residues within 4Å: Chain A: A.51, E.54, T.55 Chain C: K.40, V.41, G.42, S.43, M.44, A.52, T.55, A.56, K.59, L.96, T.98, V.99, G.100, L.101, T.127, A.130, P.131, I.132, K.133, E.136 Ligands: U-U-U-A-G-U-U.1, U-U-U-A-G-U-U.13 Protein-ligand interaction information (PLIP) not available U-U-U-A-G-U-U.8: 25 residues within 4Å: Chain D: K.40, V.41, G.42, S.43, M.44, A.52, T.55, A.56, K.59, L.96, T.98, V.99, G.100, L.101, T.127, A.130, P.131, I.132, K.133, E.136 Chain F: A.51, E.54, T.55 Ligands: U-U-U-A-G-U-U.2, U-U-U-A-G-U-U.14 Protein-ligand interaction information (PLIP) not available U-U-U-A-G-U-U.13: 25 residues within 4Å: Chain C: A.51, E.54, T.55 Chain E: K.40, V.41, G.42, S.43, M.44, A.52, T.55, A.56, K.59, L.96, T.98, V.99, G.100, L.101, T.127, A.130, P.131, I.132, K.133, E.136 Ligands: U-U-U-A-G-U-U.1, U-U-U-A-G-U-U.7 Protein-ligand interaction information (PLIP) not available U-U-U-A-G-U-U.14: 25 residues within 4Å: Chain B: A.51, E.54, T.55 Chain F: K.40, V.41, G.42, S.43, M.44, A.52, T.55, A.56, K.59, L.96, T.98, V.99, G.100, L.101, T.127, A.130, P.131, I.132, K.133, E.136 Ligands: U-U-U-A-G-U-U.2, U-U-U-A-G-U-U.8 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.137 Chain E: H.72, H.76 Ligands: HIS.4 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: HIS.4, E:H.72, E:H.76, A:H.137, H2O.29 MG.5: 4 residues within 4Å: Chain B: H.137 Chain D: H.72, H.76 Ligands: HIS.6 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: HIS.6, D:H.72, D:H.76, B:H.137, H2O.4 MG.9: 4 residues within 4Å: Chain A: H.72, H.76 Chain C: H.137 Ligands: HIS.10 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.137, A:H.72, A:H.76, HIS.10, H2O.4 MG.11: 4 residues within 4Å: Chain D: H.137 Chain F: H.72, H.76 Ligands: HIS.12 5 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: F:H.72, F:H.76, HIS.12, D:H.137, H2O.17 MG.15: 4 residues within 4Å: Chain C: H.72, H.76 Chain E: H.137 Ligands: HIS.16 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: C:H.72, C:H.76, HIS.16, E:H.137, H2O.16 MG.17: 4 residues within 4Å: Chain B: H.72, H.76 Chain F: H.137 Ligands: HIS.18 5 PLIP interactions: 1 interactions with chain F, 1 Ligand-Ligand interactions, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: F:H.137, HIS.18, B:H.72, B:H.76, H2O.29

6 x HIS: HISTIDINE(Non-covalent)

HIS.4: 11 residues within 4Å: Chain A: R.87, R.97, I.128, G.129, A.130, H.137 Chain E: Y.68, H.72, Y.75, H.76 Ligands: MG.3 9 PLIP interactions: 3 interactions with chain E, 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: E:H.76, A:A.130, H.4 Salt bridges: E:H.76, A:R.87, A:R.97, A:H.137 pi-Stacking: E:Y.75 Water bridges: A:R.97 HIS.6: 12 residues within 4Å: Chain B: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Chain D: Y.68, H.72, Y.75, H.76 Ligands: MG.5 9 PLIP interactions: 4 interactions with chain B, 4 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: B:A.130, D:Y.68, D:H.76, H.6 Salt bridges: B:R.87, B:R.97, B:H.137, D:H.76 pi-Stacking: D:Y.75 HIS.10: 11 residues within 4Å: Chain A: Y.68, H.72, Y.75, H.76 Chain C: R.87, R.97, I.128, G.129, A.130, H.137 Ligands: MG.9 9 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 5 interactions with chain C Hydrogen bonds: A:H.76, H.10, C:A.130 Salt bridges: A:H.76, C:R.87, C:R.97, C:H.137 pi-Stacking: A:Y.75 Water bridges: C:R.97 HIS.12: 12 residues within 4Å: Chain D: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Chain F: Y.68, H.72, Y.75, H.76 Ligands: MG.11 9 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions, 4 interactions with chain F Hydrogen bonds: D:A.130, H.12, F:Y.68, F:H.76 Salt bridges: D:R.87, D:R.97, D:H.137, F:H.76 pi-Stacking: F:Y.75 HIS.16: 11 residues within 4Å: Chain C: Y.68, H.72, Y.75, H.76 Chain E: R.87, R.97, I.128, G.129, A.130, H.137 Ligands: MG.15 9 PLIP interactions: 5 interactions with chain E, 3 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: E:A.130, C:H.76, H.16 Water bridges: E:R.97 Salt bridges: E:R.87, E:R.97, E:H.137, C:H.76 pi-Stacking: C:Y.75 HIS.18: 12 residues within 4Å: Chain B: Y.68, H.72, Y.75, H.76 Chain F: R.87, L.96, R.97, I.128, G.129, A.130, H.137 Ligands: MG.17 9 PLIP interactions: 4 interactions with chain F, 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: F:A.130, B:Y.68, B:H.76, H.18 Salt bridges: F:R.87, F:R.97, F:H.137, B:H.76 pi-Stacking: B:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumarevel, T. et al., Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand. Nature (2005)

Release Date

2005-03-15

Peptides

Hut operon positive regulatory protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Hut operon positive regulatory protein

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