SMTL ID : 8ju9.1

Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x KDP: 2-KETO-DEOXY-GALACTOSE(Non-covalent)

KDP.1: 19 residues within 4Å: Chain A: F.136, G.137, A.138, S.139, S.183, Q.184, S.185, G.186, S.188, T.231, T.235, P.236 Chain B: H.148, R.152, K.270, L.273, R.277 Chain D: H.164, M.168 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.273 Hydrogen bonds: B:K.270, B:R.277, A:A.138, A:S.139, A:S.183, A:S.183, A:S.183, A:Q.184, A:S.185, A:S.185, A:S.188 Salt bridges: B:H.148, B:R.152, B:K.270, B:R.277 Water bridges: A:S.139, A:T.231 KDP.5: 19 residues within 4Å: Chain A: H.148, R.152, K.270, L.273, R.277 Chain B: F.136, G.137, A.138, S.139, S.183, Q.184, S.185, G.186, S.188, T.231, T.235, P.236 Chain C: H.164, M.168 18 PLIP interactions: 11 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:A.138, B:S.139, B:S.183, B:S.183, B:S.183, B:Q.184, B:S.185, B:S.185, B:S.188, A:K.270, A:R.277 Water bridges: B:S.139, B:T.231 Hydrophobic interactions: A:L.273 Salt bridges: A:H.148, A:R.152, A:K.270, A:R.277 KDP.9: 19 residues within 4Å: Chain B: H.164, M.168 Chain C: F.136, G.137, A.138, S.139, S.183, Q.184, S.185, G.186, S.188, T.231, T.235, P.236 Chain D: H.148, R.152, K.270, L.273, R.277 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:A.138, C:S.139, C:S.183, C:S.183, C:S.183, C:Q.184, C:S.185, C:S.185, C:S.188, D:K.270, D:R.277 Water bridges: C:S.139, C:T.231 Hydrophobic interactions: D:L.273 Salt bridges: D:H.148, D:R.152, D:K.270, D:R.277 KDP.13: 19 residues within 4Å: Chain A: H.164, M.168 Chain C: H.148, R.152, K.270, L.273, R.277 Chain D: F.136, G.137, A.138, S.139, S.183, Q.184, S.185, G.186, S.188, T.231, T.235, P.236 18 PLIP interactions: 7 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:L.273 Hydrogen bonds: C:K.270, C:R.277, D:A.138, D:S.139, D:S.183, D:S.183, D:S.183, D:Q.184, D:S.185, D:S.185, D:S.188 Salt bridges: C:H.148, C:R.152, C:K.270, C:R.277 Water bridges: D:S.139, D:T.231

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

PEG.2: 6 residues within 4Å: Chain A: A.126, H.127, A.128, Q.129, L.154, R.258 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.128 PEG.3: 4 residues within 4Å: Chain A: E.108, H.112, D.226, H.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.226 PEG.6: 6 residues within 4Å: Chain B: A.126, H.127, A.128, Q.129, L.154, R.258 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.128 PEG.7: 4 residues within 4Å: Chain B: E.108, H.112, D.226, H.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.226 PEG.10: 6 residues within 4Å: Chain C: A.126, H.127, A.128, Q.129, L.154, R.258 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.128 PEG.11: 4 residues within 4Å: Chain C: E.108, H.112, D.226, H.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.226 PEG.14: 6 residues within 4Å: Chain D: A.126, H.127, A.128, Q.129, L.154, R.258 1 PLIP interactions: 1 interactions with chain D Water bridges: D:A.128 PEG.15: 4 residues within 4Å: Chain D: E.108, H.112, D.226, H.228 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.226

4 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.4: 16 residues within 4Å: Chain A: N.2, L.4, Q.5, S.73, L.74, A.75, A.76, A.78, S.79, D.232, I.233, Y.234 Chain B: V.263, L.266, K.267, K.270 No protein-ligand interaction detected (PLIP) PG5.8: 16 residues within 4Å: Chain A: V.263, L.266, K.267, K.270 Chain B: N.2, L.4, Q.5, S.73, L.74, A.75, A.76, A.78, S.79, D.232, I.233, Y.234 No protein-ligand interaction detected (PLIP) PG5.12: 16 residues within 4Å: Chain C: N.2, L.4, Q.5, S.73, L.74, A.75, A.76, A.78, S.79, D.232, I.233, Y.234 Chain D: V.263, L.266, K.267, K.270 No protein-ligand interaction detected (PLIP) PG5.16: 16 residues within 4Å: Chain C: V.263, L.266, K.267, K.270 Chain D: N.2, L.4, Q.5, S.73, L.74, A.75, A.76, A.78, S.79, D.232, I.233, Y.234 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rui, B. et al., Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence. To Be Published

Release Date

2024-01-17

Peptides

Probable transcriptional regulator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Probable transcriptional regulator