SMTL ID : 4u0w.1

Crystal structure of YvoA from Bacillus subtilis in complex with N-acetylglucosamine-6-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 16G: 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

16G.1: 18 residues within 4Å: Chain A: T.90, S.91, F.92, T.93, R.136, R.138, E.148, S.167, S.168, I.169, Y.170, Q.186, I.212, R.214, E.225, A.227, S.229, Y.231 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.212, A:Y.231 Hydrogen bonds: A:S.91, A:F.92, A:T.93, A:I.169, A:Y.170, A:Y.170, A:E.225, A:S.229, A:Y.231, A:Y.231, A:Y.231 Water bridges: A:R.138, A:S.168, A:R.214, A:R.214 Salt bridges: A:R.136, A:R.138, A:R.138, A:R.214 16G.9: 17 residues within 4Å: Chain B: S.91, F.92, T.93, R.136, R.138, E.148, S.167, S.168, I.169, Y.170, Q.186, I.212, R.214, E.225, A.227, S.229, Y.231 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.212, B:Y.231 Hydrogen bonds: B:S.91, B:S.91, B:F.92, B:T.93, B:T.93, B:I.169, B:Y.170, B:E.225, B:S.229, B:Y.231, B:Y.231 Water bridges: B:R.138, B:S.168, B:R.214, B:R.214, B:Y.231 Salt bridges: B:R.136, B:R.138, B:R.214

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.16, M.19, E.20, K.23, E.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.20 Water bridges: A:E.64, A:E.64 GOL.10: 5 residues within 4Å: Chain B: Y.16, M.19, E.20, K.23, E.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.23, B:E.64

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

EDO.3: 3 residues within 4Å: Chain A: R.183, Y.217, G.221 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: I.14, I.49, S.50, T.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.50, A:T.53, A:T.53 EDO.5: 5 residues within 4Å: Chain A: K.27, N.28, G.29, A.207, P.208 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: I.26, L.66, R.232, D.234, R.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.232, A:D.234, A:D.234 Water bridges: A:R.235 EDO.7: 4 residues within 4Å: Chain A: K.81, M.82, E.83, R.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.83, A:E.83, A:R.99 EDO.8: 4 residues within 4Å: Chain A: P.13, I.14, Y.15, T.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.14, A:Y.15 Water bridges: A:K.8, A:Q.17, A:T.53 EDO.11: 7 residues within 4Å: Chain B: E.83, Q.84, A.85, G.88, T.90, D.95, R.99 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.85, B:G.88, B:T.90, B:R.99 EDO.12: 6 residues within 4Å: Chain B: S.182, R.183, Y.217, L.218, Q.219, G.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.182, B:Q.219 Water bridges: B:R.183 EDO.13: 4 residues within 4Å: Chain B: I.113, K.133, H.151 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain B: E.118, H.151, K.228 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.118 EDO.15: 5 residues within 4Å: Chain B: I.14, I.49, S.50, T.53 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.50 EDO.16: 5 residues within 4Å: Chain B: I.26, S.78, R.232, D.234, R.235 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.78, B:D.234, B:R.235 EDO.17: 5 residues within 4Å: Chain B: P.13, I.14, Y.15, T.53 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.14, B:Y.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fillenberg, S.B. et al., Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR. Nucleic Acids Res. (2015)

Release Date

2015-01-14

Peptides

HTH-type transcriptional repressor YvoA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HTH-type transcriptional repressor YvoA

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