SMTL ID : 2igb.1

Crystal Structure of PyrR, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, UMP-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-tetramer

Ligands

4 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 12 residues within 4Å: Chain A: K.39, D.104, D.105, V.106, F.108, T.109, G.110, R.111, T.112, R.137, L.160, I.161 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.108 Hydrogen bonds: A:K.39, A:D.104, A:D.105, A:F.108, A:T.109, A:G.110, A:R.111, A:T.112, A:T.112, A:T.112, A:R.137, A:I.161, A:I.161 Water bridges: A:T.109, A:T.109, A:V.113 U5P.3: 12 residues within 4Å: Chain B: K.39, D.104, D.105, V.106, F.108, T.109, G.110, R.111, T.112, R.137, L.160, I.161 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.108 Hydrogen bonds: B:K.39, B:D.104, B:D.105, B:F.108, B:T.109, B:G.110, B:R.111, B:T.112, B:T.112, B:T.112, B:R.137, B:I.161, B:I.161 Water bridges: B:V.113 U5P.9: 12 residues within 4Å: Chain C: K.39, D.104, D.105, V.106, F.108, T.109, G.110, R.111, T.112, R.137, L.160, I.161 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.108 Hydrogen bonds: C:K.39, C:D.104, C:D.105, C:F.108, C:T.109, C:G.110, C:R.111, C:T.112, C:T.112, C:T.112, C:R.137, C:I.161, C:I.161 Water bridges: C:T.109, C:T.109, C:V.113 U5P.11: 12 residues within 4Å: Chain D: K.39, D.104, D.105, V.106, F.108, T.109, G.110, R.111, T.112, R.137, L.160, I.161 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:F.108 Hydrogen bonds: D:K.39, D:D.104, D:D.105, D:F.108, D:T.109, D:G.110, D:R.111, D:T.112, D:T.112, D:T.112, D:R.137, D:I.161, D:I.161 Water bridges: D:V.113

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

EDO.2: 6 residues within 4Å: Chain A: D.136, R.137, G.138, N.152, V.153, P.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.136 Water bridges: A:R.137 EDO.4: 4 residues within 4Å: Chain B: R.13, L.16, R.48, R.52 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.48, B:R.52, B:R.52, B:D.172 EDO.5: 4 residues within 4Å: Chain B: E.9, R.48, S.166, D.172 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.9, B:R.48, B:R.48, B:S.166 Water bridges: B:E.9, B:D.172 EDO.6: 5 residues within 4Å: Chain B: D.136, G.138, N.152, V.153, P.154 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain D: H.139, R.157 Ligands: EDO.8 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:H.139, D:R.157, D:R.157 Water bridges: B:R.128, B:R.128 EDO.8: 5 residues within 4Å: Chain B: R.26, N.27, R.128, Q.130 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.26 EDO.10: 6 residues within 4Å: Chain C: D.136, R.137, G.138, N.152, V.153, P.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.136 Water bridges: C:R.137 EDO.12: 4 residues within 4Å: Chain D: R.13, L.16, R.48, R.52 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.48, D:R.52, D:R.52, D:D.172 EDO.13: 4 residues within 4Å: Chain D: E.9, R.48, S.166, D.172 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.9, D:R.48, D:R.48, D:S.166 Water bridges: D:E.9, D:D.172 EDO.14: 5 residues within 4Å: Chain D: D.136, G.138, N.152, V.153, P.154 No protein-ligand interaction detected (PLIP) EDO.15: 3 residues within 4Å: Chain B: H.139, R.157 Ligands: EDO.16 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:H.139, B:R.157, B:R.157 Water bridges: D:R.128, D:R.128 EDO.16: 5 residues within 4Å: Chain D: R.26, N.27, R.128, Q.130 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chander, P. et al., PyrR, the regulator of the pyrimidine biosynthetic operon in Bacillus caldolyticus. To be Published

Release Date

2007-09-25

Peptides

PyrR bifunctional protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PyrR bifunctional protein

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