SMTL ID : 7na0.1

Structure of Geobacter sulfurreducens proline utilization A (PutA) variant A206W

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 33 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 Ligands: EDO.29 35 PLIP interactions: 35 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:F.433 Water bridges: A:K.331, A:R.423, A:R.423, A:E.426, A:E.426 Salt bridges: A:K.307, A:K.307, A:K.331 pi-Stacking: A:W.311, A:W.311 FAD.30: 33 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 Ligands: EDO.56 32 PLIP interactions: 32 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:Y.310, B:K.331 Salt bridges: B:K.307, B:K.307, B:K.331 pi-Stacking: B:W.311, B:W.311

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: A.309, Y.419, R.422, R.423 Ligands: EDO.29 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.204, A:R.423 Salt bridges: A:K.204, A:R.422, A:R.423 SO4.3: 4 residues within 4Å: Chain A: K.679, G.710, R.711, G.712 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.712 Water bridges: A:G.710 Salt bridges: A:K.679 SO4.31: 5 residues within 4Å: Chain B: A.309, Y.419, R.422, R.423 Ligands: EDO.56 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Y.310, B:R.423 Salt bridges: B:K.204, B:R.422, B:R.423 SO4.32: 4 residues within 4Å: Chain B: K.679, G.710, R.711, G.712 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.712 Water bridges: B:K.679, B:K.679, B:S.713, B:S.713 Salt bridges: B:K.679

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

EDO.4: 5 residues within 4Å: Chain A: T.528, V.529, I.683, A.837, D.838 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: D.146, V.147, L.148, G.149, K.204, W.207 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: E.637, T.986, N.988 Chain B: Q.320, R.946 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: Q.320, R.946 Chain B: E.637, T.986, N.988 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: D.771, L.803, D.804, A.805, K.902 Ligands: EDO.27 Ligand excluded by PLIP EDO.9: 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.10: 5 residues within 4Å: Chain A: W.655, I.683, D.838, K.840, A.841 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: Y.249, W.323, E.324, P.326, D.486, T.488 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: P.270, Q.300, I.301, I.351, H.353, R.380 Ligands: EDO.18 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: F.479, Y.617, R.620, E.621, E.954 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: F.514, G.517, L.700, P.701, E.702, G.703, V.704, F.705 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: L.68, E.71, H.72, E.75, S.926, H.929 Ligands: EDO.27 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: W.328, E.333, A.336, A.337, R.340, R.459 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: R.55 Chain B: L.638, E.987, T.989, P.996 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: F.241, H.271, H.353 Ligands: EDO.12 Ligand excluded by PLIP EDO.19: 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.20: 6 residues within 4Å: Chain A: H.499, K.584, R.585, L.586, F.587, E.588 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: Y.249, K.281, D.282, E.324, V.325, P.326 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: M.842, K.846 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: P.568, R.571, M.622, Y.643, E.644, P.645, T.672, M.980 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: K.509, T.510, Y.511, W.689 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: N.213, Q.215, P.829, N.831, Y.832 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: Y.76, R.925, P.927, L.930 Chain B: R.991 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: K.67, L.68, E.71, D.771 Ligands: EDO.8, EDO.15 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: K.756, I.757, V.966, H.978 Chain B: K.756 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: K.204, L.386, Y.407 Ligands: FAD.1, SO4.2 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain B: P.527, T.528, V.529, I.683, A.837, D.838 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: D.146, L.148, G.149, K.204, W.207 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: D.771, L.803, D.804, A.805, K.902 Ligands: EDO.46 Ligand excluded by PLIP EDO.36: 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.37: 3 residues within 4Å: Chain B: W.655, D.838, A.841 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain B: Y.249, W.323, E.324, P.326, D.486, T.488 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: P.270, Q.300, I.301, I.351, H.353, R.380 Ligands: EDO.49 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: F.479, Y.617, R.620, E.621, E.954 Ligand excluded by PLIP EDO.41: 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.42: 7 residues within 4Å: Chain B: L.68, E.71, H.72, E.75, S.926, H.929 Ligands: EDO.46 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: W.328, E.333, A.337, R.340, R.459 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain A: E.987, T.989, P.996 Chain B: R.55 Ligand excluded by PLIP EDO.45: 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.46: 6 residues within 4Å: Chain B: K.67, L.68, E.71, D.771 Ligands: EDO.35, EDO.42 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain B: H.499, K.584, R.585, L.586, F.587, E.588 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: Y.249, K.281, D.282, E.324, P.326 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain B: F.241, P.270, H.271, H.353 Ligands: EDO.39 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain B: P.568, R.571, M.622, Y.643, P.645, T.672, M.980 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain B: N.213, Q.215, D.216, P.829, A.830, N.831, Y.832 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain A: R.991 Chain B: R.55, Y.76, R.925, P.927, L.930 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain A: K.756 Chain B: K.756, I.757, V.966, H.978 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain B: K.509, T.510, Y.511, P.512 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain B: K.509, Y.511, W.592, I.686, H.690, E.693 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain B: K.204, A.309, L.386, Y.407 Ligands: FAD.30, SO4.31 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korasick, D.A. et al., Probing the function of a ligand-modulated dynamic tunnel in bifunctional proline utilization A (PutA). Arch.Biochem.Biophys. (2021)

Release Date

2021-09-22

Peptides

Bifunctional protein PutA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional protein PutA