SMTL ID : 8txl.1

Nan Regulatory Protein full length mutant R148A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 8 residues within 4Å: Chain A: R.140, K.143, L.144, M.147, E.154, A.155, L.156 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.140, A:K.143 1PE.2: 6 residues within 4Å: Chain A: A.148, F.262, Y.265, W.266, K.269 Chain B: Y.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.269

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: N.263, W.266, E.267, K.270 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.266 Hydrogen bonds: A:E.267 Salt bridges: A:K.270 ACT.10: 6 residues within 4Å: Chain B: L.180, S.181, S.206, T.223, H.224, R.232 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.180 Hydrogen bonds: B:H.224 Water bridges: B:S.206, B:H.224 Salt bridges: B:R.232

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

EDO.4: 6 residues within 4Å: Chain A: E.154, L.156, G.161, W.164, T.165 Ligands: 1PE.1 No protein-ligand interaction detected (PLIP) EDO.11: 3 residues within 4Å: Chain B: D.11, F.14, L.29 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: S.99, R.102 Chain B: S.99, R.102 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.99, A:S.99, B:S.99 Salt bridges: A:R.102, B:R.102 Water bridges: B:R.102 SO4.6: 4 residues within 4Å: Chain A: T.55, G.65, Y.66, R.67 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.55, A:Y.66, A:R.67 Water bridges: A:E.68 Salt bridges: A:R.67 SO4.7: 6 residues within 4Å: Chain A: S.135, S.179, L.180, S.181, G.182, T.184 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.135, A:S.135, A:L.180, A:S.181, A:S.181, A:S.181, A:T.184

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 6 residues within 4Å: Chain A: S.97, H.224, S.225, Q.226, R.232, I.233 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: K.200, T.216 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain B: S.97, H.224, S.225, Q.226, R.232, I.233 Ligand excluded by PLIP

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 4 residues within 4Å: Chain A: S.85, K.86, H.87 Chain B: Q.106 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.106, B:D.107, A:K.86 Salt bridges: A:H.87 PO4.17: 4 residues within 4Å: Chain B: T.55, G.65, Y.66, R.67 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.55, B:T.55, B:Y.66, B:R.67 Water bridges: B:E.68 Salt bridges: B:R.67 PO4.18: 6 residues within 4Å: Chain B: S.135, S.179, L.180, S.181, G.182, T.184 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.135, B:S.135, B:S.179, B:L.180, B:S.181, B:S.181 Water bridges: B:S.181

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain B: S.50, Q.51, A.52 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.51, B:A.52 GOL.13: 5 residues within 4Å: Chain B: S.50, A.52, A.53, R.56 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.50, B:R.56, B:R.56 GOL.14: 9 residues within 4Å: Chain B: I.6, A.7, F.28, L.29, A.31, I.34, Y.73, E.76, A.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.73, B:Y.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wood, D.M. et al., Structure of isomerase domain of the nan-regulatory protein (NanR) from Streptococcus pneumoniae. To Be Published

Release Date

2024-09-11

Peptides

Phosphosugar-binding transcriptional regulator: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphosugar-binding transcriptional regulator