SMTL ID : 3ip0.2 (1 other biounit)

Crystal structure of E. coli HPPK in complex with MgAMPCPP and 6-hydroxymethylpterin/6-carboxypterin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.89 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: R.82, D.95, D.97 Ligands: MG.2, APC.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.95, A:D.97, H2O.1, H2O.1 MG.2: 8 residues within 4Å: Chain A: R.92, D.95, D.97, R.121 Ligands: MG.1, APC.3, HHR.4, HHS.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.95, A:D.97, H2O.1 MG.13: 5 residues within 4Å: Chain B: R.82, D.95, D.97 Ligands: MG.14, APC.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.95, B:D.97, H2O.13, H2O.13 MG.14: 8 residues within 4Å: Chain B: R.92, D.95, D.97, R.121 Ligands: MG.13, APC.15, HHR.16, HHS.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.95, B:D.97, H2O.13

2 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.3: 25 residues within 4Å: Chain A: L.70, Q.74, E.77, R.82, R.84, R.88, W.89, R.92, D.95, L.96, D.97, I.98, R.110, L.111, T.112, V.113, H.115, Y.116, D.117, R.121 Ligands: MG.1, MG.2, HHR.4, HHS.5, ACT.9 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:Q.74, A:R.82, A:R.82, A:R.84, A:R.84, A:W.89, A:R.92, A:R.92, A:I.98, A:T.112, A:Y.116, A:Y.116 Water bridges: A:Q.74, A:Q.74, A:R.84, A:R.84, A:R.88, A:R.110, A:T.112, A:T.112, A:R.121, A:R.121 Salt bridges: A:H.115, A:R.121 APC.15: 25 residues within 4Å: Chain B: L.70, Q.74, E.77, R.82, R.84, R.88, W.89, R.92, D.95, L.96, D.97, I.98, R.110, L.111, T.112, V.113, H.115, Y.116, D.117, R.121 Ligands: MG.13, MG.14, HHR.16, HHS.17, ACT.21 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:Q.74, B:R.82, B:R.82, B:R.84, B:R.84, B:W.89, B:R.92, B:R.92, B:I.98, B:T.112, B:Y.116, B:Y.116 Water bridges: B:Q.74, B:Q.74, B:R.84, B:R.84, B:R.88, B:R.110, B:T.112, B:T.112, B:H.115, B:H.115, B:R.121, B:R.121 Salt bridges: B:H.115, B:R.121

2 x HHR: 6-HYDROXYMETHYLPTERIN(Non-covalent)

HHR.4: 16 residues within 4Å: Chain A: G.8, T.42, P.43, P.44, L.45, G.46, Y.53, N.55, W.89, R.92, D.95, R.121, F.123 Ligands: MG.2, APC.3, HHS.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.42, A:T.42, A:L.45, A:N.55, A:N.55, A:R.92, A:R.92, A:R.92 Water bridges: A:G.46, A:G.46, A:R.121, A:R.121 pi-Stacking: A:Y.53, A:F.123 pi-Cation interactions: A:Y.53, A:F.123 HHR.16: 16 residues within 4Å: Chain B: G.8, T.42, P.43, P.44, L.45, G.46, Y.53, N.55, W.89, R.92, D.95, R.121, F.123 Ligands: MG.14, APC.15, HHS.17 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.42, B:T.42, B:L.45, B:N.55, B:N.55, B:R.92, B:R.92, B:R.92 Water bridges: B:G.46, B:G.46, B:R.121, B:R.121 pi-Stacking: B:Y.53, B:F.123 pi-Cation interactions: B:Y.53, B:F.123

2 x HHS: 6-CARBOXYPTERIN(Non-covalent)

HHS.5: 15 residues within 4Å: Chain A: G.8, T.42, P.43, P.44, L.45, Y.53, N.55, W.89, R.92, D.95, R.121, F.123 Ligands: MG.2, APC.3, HHR.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.42, A:T.42, A:L.45, A:N.55, A:N.55, A:R.92, A:D.95 Water bridges: A:G.46, A:W.89, A:R.121, A:R.121 Salt bridges: A:R.92, A:R.121 pi-Stacking: A:Y.53, A:F.123 pi-Cation interactions: A:Y.53, A:F.123 HHS.17: 15 residues within 4Å: Chain B: G.8, T.42, P.43, P.44, L.45, Y.53, N.55, W.89, R.92, D.95, R.121, F.123 Ligands: MG.14, APC.15, HHR.16 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.42, B:T.42, B:L.45, B:N.55, B:N.55, B:R.92, B:D.95 Water bridges: B:G.46, B:W.89, B:R.121, B:R.121 Salt bridges: B:R.92, B:R.121 pi-Stacking: B:Y.53, B:F.123 pi-Cation interactions: B:Y.53, B:F.123

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

CL.6: 5 residues within 4Å: Chain A: P.114, K.119, F.137, P.138, D.139 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: T.112, Y.116 Chain B: T.112, Y.116 Ligands: CL.19 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain A: G.46, P.47, Q.48 Chain B: G.46, P.47, Q.48 Ligands: CL.20 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: P.114, K.119, F.137, P.138, D.139 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: T.112, Y.116 Chain B: T.112, Y.116 Ligands: CL.7 Ligand excluded by PLIP CL.20: 7 residues within 4Å: Chain A: G.46, P.47, Q.48 Chain B: G.46, P.47, Q.48 Ligands: CL.8 Ligand excluded by PLIP

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

ACT.9: 4 residues within 4Å: Chain A: T.112, Y.116 Chain B: N.120 Ligands: APC.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.115 ACT.10: 6 residues within 4Å: Chain A: E.30, S.31, H.32, E.61, T.62, S.63 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.30 Salt bridges: A:H.32 ACT.11: 3 residues within 4Å: Chain A: W.126, F.129, K.154 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.154 Salt bridges: A:K.154 ACT.12: 2 residues within 4Å: Chain A: L.11, P.51 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.11 ACT.21: 4 residues within 4Å: Chain A: N.120 Chain B: T.112, Y.116 Ligands: APC.15 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.115, B:H.115 Salt bridges: B:H.115 ACT.22: 6 residues within 4Å: Chain B: E.30, S.31, H.32, E.61, T.62, S.63 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.30 Salt bridges: B:H.32 ACT.23: 3 residues within 4Å: Chain B: W.126, F.129, K.154 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.154 Salt bridges: B:K.154 ACT.24: 2 residues within 4Å: Chain B: L.11, P.51 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaszczyk, J. et al., Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydroptein pyrophosphokinase: Crystallographic studies. Biochemistry (2003)

Release Date

2009-08-25

Peptides

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

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