SMTL ID : 4mgh.1

Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight from Xenon Trapping and Statistical Coupling Analysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

ADP.1: 19 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, S.894 Ligands: MG.2, MG.3, MG.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.394, A:T.394, A:G.395, A:Y.396, A:Q.676, A:A.686, A:N.730, A:N.730, A:S.894 Water bridges: A:V.654, A:D.895 Salt bridges: A:K.657

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.687, N.730, D.892, S.894 Ligands: ADP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.687, A:D.892, H2O.20 MG.3: 2 residues within 4Å: Chain A: E.726 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.726, H2O.3, H2O.4, H2O.17 MG.4: 2 residues within 4Å: Chain A: E.904 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)

13 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:H.304 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.303, A:N.305, A:H.306, A:S.786, A:S.786 Water bridges: A:K.417 Salt bridges: A:H.224 SO4.9: 5 residues within 4Å: Chain A: Q.1184, Q.1191, G.1192, M.1193, V.1194 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.1184, A:G.1192, A:V.1194 Water bridges: A:S.1030, A:Q.1191, A:G.1192 SO4.10: 3 residues within 4Å: Chain A: P.1048, K.1049, H.1094 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.1049, A:N.1092 Water bridges: A:H.1094 Salt bridges: A:K.1049 SO4.11: 4 residues within 4Å: Chain A: H.1094, R.1134, P.1135, Q.1136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.1136, A:Q.1136 Salt bridges: A:H.1094, A:R.1134 SO4.12: 2 residues within 4Å: Chain A: N.1121, R.1123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.1121, A:N.1121 Salt bridges: A:R.1123 SO4.13: 3 residues within 4Å: Chain A: G.921, D.922, D.923 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.922, A:D.923 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:F.1173 Salt bridges: A:R.1167 SO4.15: 5 residues within 4Å: Chain A: S.20, A.21, F.22, N.1006, H.1169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.22, A:N.1006 Salt bridges: A:H.1169 SO4.16: 2 residues within 4Å: Chain A: T.640, I.641 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.641 SO4.17: 3 residues within 4Å: Chain A: R.1153, R.1164, R.1212 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.1153, A:R.1164, A:R.1212 SO4.18: 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 SO4.19: 2 residues within 4Å: Chain A: K.1236, V.1237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.1237

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

ACT.20: 8 residues within 4Å: Chain A: V.446, G.449, P.450, A.451, L.516, I.538, L.539, R.558 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.446, A:I.538, A:L.539 Hydrogen bonds: A:A.451, A:L.539 Salt bridges: A:R.558 ACT.21: 3 residues within 4Å: Chain A: T.1183, Q.1184, R.1229 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.1184 Salt bridges: A:R.1229 ACT.22: 6 residues within 4Å: Chain A: E.656, T.658, W.681, Q.682, E.1013, K.1017 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.658 Hydrogen bonds: A:Q.682, A:E.1013 Water bridges: A:R.1176 Salt bridges: A:K.1017 ACT.23: 2 residues within 4Å: Chain A: H.76, T.77 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.76 Hydrogen bonds: A:S.75, A:T.77 Salt bridges: A:H.76

4 x XE: XENON(Non-covalent)

XE.24: 4 residues within 4Å: Chain A: F.1068, L.1096, L.1138, L.1140 No protein-ligand interaction detected (PLIP) XE.25: 5 residues within 4Å: Chain A: I.425, A.689, T.691, E.701, M.703 No protein-ligand interaction detected (PLIP) XE.26: 3 residues within 4Å: Chain A: L.198, F.202, F.217 No protein-ligand interaction detected (PLIP) XE.27: 3 residues within 4Å: Chain A: K.886, A.946, V.947 No protein-ligand interaction detected (PLIP)

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

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