SMTL ID : 4nm9.1

Crystal structure of the resting state of proline utilization A (PutA) from Geobacter sulfurreducens PCA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 32 residues within 4Å: Chain A: K.204, D.245, M.246, V.275, Q.277, Y.279, R.304, V.306, K.307, G.308, A.309, Y.310, W.311, W.328, T.329, I.330, K.331, S.334, D.335, A.357, S.358, H.359, N.360, Q.384, V.385, L.386, Y.407, R.423, E.426, E.431, S.432, F.433 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:A.357, A:Q.384, A:L.386, A:L.386, A:Y.407, A:Y.407 Hydrogen bonds: A:K.204, A:M.246, A:M.246, A:Q.277, A:R.304, A:K.307, A:G.308, A:G.308, A:G.308, A:A.309, A:T.329, A:S.334, A:D.335, A:H.359, A:H.359, A:N.360, A:N.360, A:E.426, A:E.426, A:F.433 Water bridges: A:K.331, A:L.434 Salt bridges: A:K.307, A:K.307, A:K.331 pi-Stacking: A:W.311, A:W.311 FAD.14: 32 residues within 4Å: Chain B: K.204, D.245, M.246, V.275, Q.277, Y.279, R.304, V.306, K.307, G.308, A.309, Y.310, W.311, W.328, T.329, I.330, K.331, S.334, D.335, A.357, S.358, H.359, N.360, Q.384, V.385, L.386, Y.407, R.423, E.426, E.431, S.432, F.433 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:A.357, B:Q.384, B:L.386, B:L.386, B:Y.407, B:Y.407 Hydrogen bonds: B:K.204, B:M.246, B:M.246, B:Q.277, B:R.304, B:K.307, B:G.308, B:G.308, B:G.308, B:A.309, B:T.329, B:S.334, B:D.335, B:S.358, B:H.359, B:N.360, B:N.360, B:E.426, B:F.433 Water bridges: B:K.331 Salt bridges: B:K.307, B:K.307, B:K.331 pi-Stacking: B:W.311, B:W.311

22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: Y.249, W.323, E.324, D.486, T.488 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: Q.320, R.946 Chain B: E.637, T.986, N.988 Ligand excluded by PLIP EDO.4: 10 residues within 4Å: Chain A: E.610, F.614, A.951, L.952, V.953, Q.956, P.957, F.958, A.970, G.971 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: A.911, N.912, T.914, F.916, A.917, R.938, V.939, R.962 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: W.328, E.333, A.336, A.337, R.340, R.459 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: G.636, E.637, T.986, N.988 Chain B: Q.320, R.946 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: K.756, I.757, V.966, H.978 Chain B: K.756 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: P.270, Q.300, I.301, I.351, H.353, R.380 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: F.479, Y.617, R.620, E.621, E.954 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: M.484, D.602, Q.603, A.606, Y.784 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: H.499, K.584, R.585, L.586, F.587, E.588 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: I.652, G.716, D.717, R.739, I.740 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: D.771, L.803, D.804, A.805, K.902 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain B: D.804 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain B: E.610, F.614, A.951, L.952, V.953, Q.956, P.957, F.958, A.970, G.971 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: Y.249, W.323, E.324, P.326, D.486, T.488 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain B: A.911, N.912, T.914, F.916, A.917, F.937, R.938, V.939, R.962 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: W.328, E.333, A.336, A.337, R.340, R.459 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: K.756 Chain B: K.756, I.757, V.966, H.978 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: F.514, G.517, L.700, P.701, E.702, G.703, V.704, F.705 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: P.270, Q.300, I.301, I.351, H.353, R.380 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: F.479, Y.617, R.620, E.621, E.954 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, H. et al., Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-02-19

Peptides

Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase

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