SMTL ID : 3e2q.1 (1 other biounit)

Crystal Structure Reduced PutA86-630 Mutant Y540S Complexed with trans-4-hydroxy-L-proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 30 residues within 4Å: Chain A: D.285, A.286, V.317, Q.319, Y.321, V.348, K.349, G.350, A.351, Y.352, W.353, Y.371, T.372, R.373, K.374, T.377, D.378, A.400, T.401, H.402, N.403, Q.426, C.427, L.428, S.455, E.474, T.479, S.480, F.481 Ligands: HYP.2 33 PLIP interactions: 31 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:A.400, A:Q.426, A:L.428 Hydrogen bonds: A:A.286, A:A.286, A:Q.319, A:K.349, A:G.350, A:G.350, A:G.350, A:A.351, A:T.372, A:D.378, A:T.401, A:T.401, A:H.402, A:N.403, A:N.403, A:E.474, A:T.479, A:F.481 Water bridges: A:N.283, A:K.374, A:E.474, A:E.474, A:V.482, P.2, P.2 Salt bridges: A:K.349, A:K.349, A:K.374 pi-Stacking: A:W.353, A:W.353 FAD.5: 30 residues within 4Å: Chain B: D.285, A.286, V.317, Q.319, Y.321, V.348, K.349, G.350, A.351, Y.352, W.353, Y.371, T.372, R.373, K.374, T.377, D.378, A.400, T.401, H.402, N.403, Q.426, C.427, L.428, S.455, E.474, T.479, S.480, F.481 Ligands: HYP.6 33 PLIP interactions: 31 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:A.400, B:Q.426, B:L.428 Hydrogen bonds: B:A.286, B:A.286, B:Q.319, B:K.349, B:G.350, B:G.350, B:G.350, B:A.351, B:T.372, B:D.378, B:T.401, B:T.401, B:H.402, B:N.403, B:N.403, B:E.474, B:T.479, B:F.481 Water bridges: B:N.283, B:K.374, B:E.474, B:E.474, B:V.482, P.6, P.6 Salt bridges: B:K.349, B:K.349, B:K.374 pi-Stacking: B:W.353, B:W.353

2 x HYP: 4-HYDROXYPROLINE(Non-covalent)

HYP.2: 10 residues within 4Å: Chain A: D.200, K.244, D.285, A.351, L.428, S.455, Y.467, R.470, R.471 Ligands: FAD.1 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:L.428, A:Y.467 Hydrogen bonds: A:K.244, A:K.244, A:S.455, A:S.455, P.2, P.2 Water bridges: A:R.346, A:R.346, P.2 Salt bridges: A:K.244, A:R.470, A:R.471 HYP.6: 10 residues within 4Å: Chain B: D.200, K.244, D.285, A.351, L.428, S.455, Y.467, R.470, R.471 Ligands: FAD.5 14 PLIP interactions: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:L.428, B:Y.467 Hydrogen bonds: B:K.244, B:K.244, B:S.455, B:S.455, P.6, P.6 Water bridges: B:R.346, B:R.346, P.6 Salt bridges: B:K.244, B:R.470, B:R.471

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

1PE.3: 9 residues within 4Å: Chain A: L.169, M.170, Q.173, F.174, L.472, N.475 Chain B: R.59, E.85, R.89 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.169, A:N.475, A:N.475, B:R.59 Water bridges: A:Q.173, B:R.59 1PE.4: 2 residues within 4Å: Chain A: L.389, L.413 No protein-ligand interaction detected (PLIP) 1PE.7: 9 residues within 4Å: Chain A: R.59, E.85, R.89 Chain B: L.169, M.170, Q.173, F.174, L.472, N.475 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.59, B:L.169, B:N.475, B:N.475 Water bridges: A:R.59, B:Q.173 1PE.8: 2 residues within 4Å: Chain B: L.389, L.413 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ostrander, E.L. et al., A conserved active site tyrosine residue of proline dehydrogenase helps enforce the preference for proline over hydroxyproline as the substrate. Biochemistry (2009)

Release Date

2009-02-03

Peptides

Proline dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proline dehydrogenase

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