SMTL ID : 1ecc.1

ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE COMPLEXED WITH MN-CPRPP AND 5-OXO-NORLEUCINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: P.302, D.366, D.367 Ligands: PCP.4 No protein-ligand interaction detected (PLIP) MN.2: 1 residues within 4Å: Chain A: E.449 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.449 MN.5: 3 residues within 4Å: Chain B: D.366, D.367 Ligands: PCP.9 No protein-ligand interaction detected (PLIP) MN.6: 2 residues within 4Å: Chain B: E.376, I.428 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.376, B:I.428 MN.7: 2 residues within 4Å: Chain B: N.277, E.449 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.449, H2O.9, H2O.12, H2O.12, H2O.12 MN.10: 4 residues within 4Å: Chain C: P.302, D.366, D.367 Ligands: PCP.13 No protein-ligand interaction detected (PLIP) MN.11: 1 residues within 4Å: Chain C: E.449 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.449 MN.14: 3 residues within 4Å: Chain D: D.366, D.367 Ligands: PCP.18 No protein-ligand interaction detected (PLIP) MN.15: 2 residues within 4Å: Chain D: E.376, I.428 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.376, D:I.428 MN.16: 2 residues within 4Å: Chain D: N.277, E.449 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.449, H2O.21, H2O.23, H2O.23, H2O.23

4 x ONL: 5-OXO-L-NORLEUCINE(Covalent)

ONL.3: 13 residues within 4Å: Chain A: C.1, R.73, Y.74, P.75, T.76, A.77, Q.86, H.100, N.101, G.102, N.103, D.127, S.128 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.74, A:T.76 Hydrogen bonds: A:T.76, A:T.76, A:A.77, A:Q.86, A:N.101, A:G.102, A:D.127, A:S.128, A:S.128 Water bridges: A:R.26 Salt bridges: A:R.73 ONL.8: 12 residues within 4Å: Chain B: C.1, R.73, Y.74, T.76, A.77, Q.86, H.100, N.101, G.102, N.103, D.127, S.128 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.74 Hydrogen bonds: B:C.1, B:T.76, B:A.77, B:Q.86, B:N.101, B:G.102, B:D.127, B:S.128, B:S.128 Water bridges: B:S.126 Salt bridges: B:R.73 ONL.12: 13 residues within 4Å: Chain C: C.1, R.73, Y.74, P.75, T.76, A.77, Q.86, H.100, N.101, G.102, N.103, D.127, S.128 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.74, C:T.76 Hydrogen bonds: C:T.76, C:A.77, C:Q.86, C:N.101, C:G.102, C:D.127, C:S.128, C:S.128 Water bridges: C:R.26 Salt bridges: C:R.73 ONL.17: 12 residues within 4Å: Chain D: C.1, R.73, Y.74, T.76, A.77, Q.86, H.100, N.101, G.102, N.103, D.127, S.128 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.74 Hydrogen bonds: D:T.76, D:A.77, D:Q.86, D:N.101, D:G.102, D:D.127, D:S.128, D:S.128 Water bridges: D:S.126 Salt bridges: D:R.73

4 x PCP: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE(Non-covalent)

PCP.4: 19 residues within 4Å: Chain A: Y.258, P.302, E.303, T.304, R.332, T.333, F.334, K.349, D.366, D.367, S.368, I.369, V.370, R.371, G.372, T.373, T.374 Chain B: R.328 Ligands: MN.1 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.334 Hydrogen bonds: A:Y.258, A:E.303, A:T.304, A:T.304, A:T.333, A:F.334, A:V.370, A:R.371, A:R.371, A:G.372, A:T.373, A:T.374, A:T.374 Water bridges: A:S.305, A:K.326, A:D.367, A:T.373, A:T.373, A:S.375 Salt bridges: A:R.332, A:K.349, A:K.349, B:R.328 PCP.9: 19 residues within 4Å: Chain A: R.328 Chain B: Y.258, P.302, E.303, T.304, R.332, T.333, F.334, K.349, D.366, D.367, S.368, I.369, V.370, R.371, G.372, T.373, T.374 Ligands: MN.5 27 PLIP interactions: 26 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.334 Hydrogen bonds: B:Y.258, B:Y.258, B:P.302, B:E.303, B:T.304, B:T.304, B:T.333, B:F.334, B:V.370, B:R.371, B:G.372, B:T.373, B:T.374, B:T.374 Water bridges: B:T.333, B:T.333, B:K.349, B:R.371, B:T.373, B:T.373, B:T.374, B:S.375 Salt bridges: B:R.332, B:K.349, B:K.349, A:R.328 PCP.13: 19 residues within 4Å: Chain C: Y.258, P.302, E.303, T.304, R.332, T.333, F.334, K.349, D.366, D.367, S.368, I.369, V.370, R.371, G.372, T.373, T.374 Chain D: R.328 Ligands: MN.10 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.334 Hydrogen bonds: C:Y.258, C:Y.258, C:E.303, C:T.304, C:T.304, C:T.333, C:F.334, C:V.370, C:R.371, C:R.371, C:G.372, C:T.373, C:T.373, C:T.374, C:T.374 Water bridges: C:S.305, C:K.326, C:T.373, C:S.375 Salt bridges: C:R.332, C:K.349, C:K.349, D:R.328 PCP.18: 19 residues within 4Å: Chain C: R.328 Chain D: Y.258, P.302, E.303, T.304, R.332, T.333, F.334, K.349, D.366, D.367, S.368, I.369, V.370, R.371, G.372, T.373, T.374 Ligands: MN.14 29 PLIP interactions: 28 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.334 Hydrogen bonds: D:Y.258, D:P.302, D:E.303, D:T.304, D:T.304, D:T.304, D:T.333, D:F.334, D:D.366, D:V.370, D:R.371, D:G.372, D:T.373, D:T.373, D:T.374, D:T.374 Water bridges: D:K.349, D:D.367, D:D.367, D:R.371, D:T.373, D:T.373, D:T.374, D:S.375 Salt bridges: D:R.332, D:K.349, D:K.349, C:R.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krahn, J.M. et al., Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry (1997)

Release Date

1998-04-15

Peptides

GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE

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