SMTL ID : 4p86.1

Structure of PyrR protein from Bacillus subtilis with GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

6 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 12 residues within 4Å: Chain A: K.41, D.106, D.107, V.108, Y.110, T.111, G.112, R.113, T.114, R.139, K.162, V.163 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:K.41, A:D.106, A:D.107, A:Y.110, A:T.111, A:T.111, A:T.111, A:G.112, A:R.113, A:T.114, A:T.114, A:R.139, A:V.163, A:V.163, A:V.163 Water bridges: A:T.111, A:T.111, A:V.115 Salt bridges: A:D.107 pi-Cation interactions: A:K.162 5GP.3: 13 residues within 4Å: Chain B: K.41, D.106, D.107, V.108, Y.110, T.111, G.112, R.113, T.114, R.139, K.162, V.163, V.165 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:K.41, B:D.106, B:D.107, B:Y.110, B:T.111, B:T.111, B:T.111, B:G.112, B:R.113, B:T.114, B:T.114, B:R.139, B:V.163, B:V.163, B:V.163, B:V.165 Water bridges: B:V.115 Salt bridges: B:D.107 5GP.4: 15 residues within 4Å: Chain B: H.141, P.156, T.157, S.158, E.161 Chain C: K.5, A.6, I.8, K.153, I.155, P.156, T.157, E.161, I.178 Ligands: 5GP.5 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Water bridges: B:K.159 Salt bridges: B:H.141, C:E.161 Hydrogen bonds: C:K.5, C:K.153, C:N.154, C:P.156 5GP.5: 13 residues within 4Å: Chain B: A.6, I.8, K.153, P.156, T.157, E.161 Chain C: K.5, H.141, P.156, T.157, S.158, E.161 Ligands: 5GP.4 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.153, B:K.153, B:P.156, C:K.5 Salt bridges: B:E.161, C:H.141 5GP.6: 13 residues within 4Å: Chain C: K.41, D.106, D.107, V.108, Y.110, T.111, G.112, R.113, T.114, R.139, K.162, V.163, V.165 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:K.41, C:D.106, C:D.107, C:Y.110, C:T.111, C:T.111, C:T.111, C:G.112, C:R.113, C:T.114, C:T.114, C:R.139, C:V.163, C:V.163, C:V.163, C:V.165 Water bridges: C:V.115 Salt bridges: C:D.107 5GP.7: 13 residues within 4Å: Chain D: K.41, D.106, D.107, V.108, Y.110, T.111, G.112, R.113, T.114, R.139, K.162, V.163, V.165 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:K.41, D:D.106, D:D.107, D:Y.110, D:T.111, D:T.111, D:T.111, D:G.112, D:R.113, D:T.114, D:T.114, D:R.139, D:K.162, D:V.163, D:V.163, D:V.163, D:V.165 Water bridges: D:V.115 Salt bridges: D:D.107 pi-Cation interactions: D:K.162, D:K.162

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.19, H.23, R.54, I.58 Chain C: H.23, I.58 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.54, C:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perica, T. et al., Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science (2014)

Release Date

2014-12-17

Peptides

Bifunctional protein PyrR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Bifunctional protein PyrR

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