SMTL ID : 4u0v.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x GLP: 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GLP.1: 15 residues within 4Å: Chain A: S.91, F.92, T.93, R.136, R.138, E.148, S.167, S.168, I.169, Y.170, R.214, E.225, A.227, Y.231 Ligands: EDO.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.91, A:S.91, A:F.92, A:T.93, A:T.93, A:E.148, A:I.169, A:Y.170, A:R.214, A:E.225, A:Y.231, A:Y.231 Water bridges: A:R.138, A:S.168, A:R.214, A:R.214, A:R.214, A:R.214 Salt bridges: A:R.136, A:R.138, A:R.138, A:R.214 GLP.15: 15 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, R.214, E.225, A.227, Y.231 Ligands: EDO.26 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.91, B:F.92, B:T.93, B:E.148, B:I.169, B:Y.170, B:Y.170, B:E.225, B:Y.231 Water bridges: B:R.138, B:S.168, B:R.214, B:R.214, B:S.229, B:Y.231 Salt bridges: B:R.136, B:R.138, B:R.138, B:R.214

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

EDO.2: 7 residues within 4Å: Chain A: L.86, Q.186, I.212, R.214, Y.231 Chain B: M.242 Ligands: GLP.1 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: Q.87, Y.241, M.242, D.243 Chain B: Q.87 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: Y.16, M.19, E.20, K.23 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: S.182, L.218, Q.219, G.221 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: Y.176, N.177 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: L.160, F.165 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: I.113, L.119, K.133, H.151 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: E.187, E.189, L.211, K.213 Chain B: T.237 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: P.13, I.14, Y.15, T.53 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: E.189, P.190, S.191 Ligands: EDO.13 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.20, K.23, T.24, K.27 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: S.191, A.192, E.197, V.209, V.230 Ligands: EDO.11 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: E.94, Y.170, D.171, E.174 Chain B: R.244 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: Y.16, M.19, E.20, K.23, E.64 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain B: N.220 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: E.155, Y.176, N.177 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: L.156, N.177, L.218, N.220, T.222 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: S.191, A.192, T.194, E.197, V.209, V.230 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: K.185, T.215, Y.217 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: P.13, I.14, Y.15, T.53 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: T.237 Chain B: E.187, E.189, L.211, K.213 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: R.244 Chain B: S.91, E.94, Y.170, D.171, E.174 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: G.88, L.89, T.90 Chain B: D.243, R.244 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: M.242 Chain B: Q.84, L.86, Q.186, I.212, R.214, Y.231 Ligands: GLP.15 Ligand excluded by PLIP

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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