SMTL ID : 4l78.1

Xenon Trapping and Statistical Coupling Analysis Uncover Regions Important for Structure and Function of Multidomain Protein StPurL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: V.341, F.343, T.394, G.395, Y.396, F.397, K.657, L.660, V.661, Q.676, P.684, A.686, D.687, E.726, N.730, D.892, S.894 Ligands: MG.2, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.394, A:T.394, A:G.395, A:Y.396, A:Y.396, A:Q.676, A:Q.676, A:N.730, A:S.894 Water bridges: A:K.657, A:K.657, A:K.657, A:D.895 Salt bridges: A:K.657

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: D.687, N.730, D.892 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.687, A:D.892, H2O.2, H2O.4 MG.3: 2 residues within 4Å: Chain A: E.726 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.726, H2O.3, H2O.5, H2O.6, H2O.25 MG.4: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: Y.259 No protein-ligand interaction detected (PLIP)

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 2 residues within 4Å: Chain A: K.841, H.843 No protein-ligand interaction detected (PLIP)

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

SO4.7: 5 residues within 4Å: Chain A: H.224, E.302, G.512, A.513, K.784 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.513 Water bridges: A:D.510 Salt bridges: A:H.224, A:K.784 SO4.8: 6 residues within 4Å: Chain A: H.224, T.303, H.304, N.305, H.306, S.786 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.303, A:N.305, A:H.306, A:S.786, A:S.786 SO4.9: 2 residues within 4Å: Chain A: K.1236, V.1237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.1237 SO4.10: 5 residues within 4Å: Chain A: Q.1184, Q.1191, G.1192, M.1193, V.1194 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.1184, A:G.1192, A:V.1194 Water bridges: A:G.1192, A:V.1194 SO4.11: 4 residues within 4Å: Chain A: P.1048, K.1049, N.1092, H.1094 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.1049 Salt bridges: A:K.1049, A:H.1094 SO4.12: 5 residues within 4Å: Chain A: H.1094, R.1134, P.1135, Q.1136, T.1137 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.1136, A:T.1137 Water bridges: A:H.1094, A:R.1134, A:R.1134 Salt bridges: A:H.1094, A:R.1134 SO4.13: 2 residues within 4Å: Chain A: N.1121, R.1123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1121 Salt bridges: A:R.1123 SO4.14: 3 residues within 4Å: Chain A: W.313, R.1167, R.1172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.1172 Water bridges: A:R.1167, A:R.1172 Salt bridges: A:R.1167 SO4.15: 5 residues within 4Å: Chain A: S.20, A.21, F.22, N.1006, H.1169 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.22, A:N.1006 Water bridges: A:S.20, A:S.20 Salt bridges: A:H.1169 SO4.16: 4 residues within 4Å: Chain A: P.364, E.365, R.366, W.793 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.365, A:R.366 Water bridges: A:E.365, A:Q.794 Salt bridges: A:R.366 SO4.17: 2 residues within 4Å: Chain A: T.640, I.641 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.641 SO4.18: 3 residues within 4Å: Chain A: A.919, V.960, H.961 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.960, A:Y.962 Salt bridges: A:H.961

5 x XE: XENON(Non-covalent)

XE.19: 5 residues within 4Å: Chain A: F.1068, L.1096, L.1138, A.1139, L.1140 No protein-ligand interaction detected (PLIP) XE.20: 5 residues within 4Å: Chain A: I.425, A.689, T.691, E.701, M.703 No protein-ligand interaction detected (PLIP) XE.21: 4 residues within 4Å: Chain A: L.198, F.202, F.217, L.608 No protein-ligand interaction detected (PLIP) XE.22: 2 residues within 4Å: Chain A: K.886, A.946 No protein-ligand interaction detected (PLIP) XE.23: 5 residues within 4Å: Chain A: E.11, L.13, H.47, A.49, L.67 No protein-ligand interaction detected (PLIP)

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

CL.24: 3 residues within 4Å: Chain A: R.30, A.34, E.138 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: H.306, A.309 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain A: Y.215, A.218, Q.219 Ligand excluded by PLIP

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

ACT.27: 4 residues within 4Å: Chain A: V.440, T.589, E.590, E.591 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.590, A:E.591 ACT.28: 2 residues within 4Å: Chain A: H.76, T.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.77 Salt bridges: A:H.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanwar, A.S. et al., Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis. Plos One (2013)

Release Date

2013-12-11

Peptides

Phosphoribosylformylglycinamidine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoribosylformylglycinamidine synthase