SMTL ID : 6pd2.2 (1 other biounit)

PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (AEP) transaminase from Treponema denticola in complex with cytidine monophosphate-AEP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 15 residues within 4Å: Chain A: S.313, G.314, T.315, D.318, Y.340, R.343, H.388, T.390, D.415, V.417, S.418, K.441 Chain B: F.489, T.490 Ligands: PO4.4 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.340, A:V.417 Hydrogen bonds: A:G.314, A:T.315, A:S.418, A:S.418, A:K.441, B:T.490, B:T.490 Water bridges: A:R.343, A:T.438, A:T.438, A:N.440, B:R.276 pi-Stacking: A:Y.340 PLP.14: 16 residues within 4Å: Chain A: F.489, T.490 Chain B: S.313, G.314, T.315, D.318, Y.340, R.343, V.386, H.388, T.390, D.415, V.417, S.418, K.441 Ligands: PO4.21 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.340, B:V.386, B:V.417 Hydrogen bonds: B:G.314, B:T.315, B:T.390, B:K.441, A:T.490, A:T.490 Water bridges: B:Y.340, B:R.343, B:R.343, B:N.440, B:N.440 Salt bridges: B:K.441 pi-Stacking: B:Y.340

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.25, D.106, E.220, D.222 Ligands: MG.3, 0RC.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.106, A:E.220, A:D.222, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.136, E.220, D.222 Ligands: MG.2, 0RC.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.136, A:E.220, A:E.220, A:D.222, H2O.1 MG.13: 5 residues within 4Å: Chain B: D.136, E.220, D.222 Ligands: MG.15, 0RC.17 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.136, B:E.220, B:E.220, B:D.222, H2O.16 MG.15: 5 residues within 4Å: Chain B: D.106, E.220, D.222 Ligands: MG.13, 0RC.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.106, B:E.220, B:D.222, H2O.14

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: Y.340, Y.575 Chain B: R.276, T.490 Ligands: PLP.1 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.340, A:Y.340, B:T.490 Water bridges: A:R.343, A:R.343, A:Y.575, A:Y.575, A:K.578, A:R.586, A:R.586, B:R.276, B:R.276, B:R.276 Salt bridges: A:K.578, B:R.276 PO4.8: 4 residues within 4Å: Chain A: G.13, S.14, R.15 Ligands: 0RC.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.14, A:R.15 Water bridges: A:L.12, A:K.25, A:K.25 Salt bridges: A:R.15, A:K.25 PO4.12: 5 residues within 4Å: Chain A: P.553, E.554, T.555, P.556, Y.558 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.556 Water bridges: A:D.583 PO4.16: 2 residues within 4Å: Chain B: L.12 Ligands: 0RC.17 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.25 PO4.21: 5 residues within 4Å: Chain A: R.276 Chain B: Y.340, K.441, Y.575 Ligands: PLP.14 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:T.490, B:Y.340, B:Y.340, B:Y.575 Water bridges: A:T.490, B:Y.340, B:R.343, B:R.343, B:R.343, B:K.578, B:R.586, B:R.586 Salt bridges: A:R.276, B:K.441, B:K.578 PO4.26: 4 residues within 4Å: Chain B: E.554, T.555, P.556, Y.558 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.554

2 x 0RC: 5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine(Non-covalent)

0RC.5: 25 residues within 4Å: Chain A: L.8, A.9, G.10, G.11, R.15, K.25, Y.80, T.83, G.84, S.85, T.88, E.104, S.105, D.106, D.136, V.138, K.153, L.165, E.194, E.196, E.220, D.222 Ligands: MG.2, MG.3, PO4.8 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.10, A:G.11, A:R.15, A:K.25, A:T.83, A:T.88, A:S.105, A:S.105, A:S.105, A:D.136, A:K.153, A:E.196 Water bridges: A:G.13 Salt bridges: A:K.25 0RC.17: 23 residues within 4Å: Chain B: L.8, A.9, G.10, G.11, K.25, Y.80, T.83, G.84, S.85, T.88, E.104, S.105, D.106, D.136, V.138, K.153, L.165, E.196, E.220, D.222 Ligands: MG.13, MG.15, PO4.16 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.10, B:G.11, B:T.83, B:T.88, B:S.105, B:S.105, B:D.136, B:K.153, B:E.196, B:E.196 Water bridges: B:A.9, B:G.11, B:G.11, B:S.85 Salt bridges: B:K.25

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

EDO.6: 8 residues within 4Å: Chain A: D.272, I.273, V.493, Q.494 Chain B: L.252, P.257, A.258, T.260 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.273, A:I.273, A:Q.494, B:T.260 EDO.7: 7 residues within 4Å: Chain A: C.288, T.307, V.308, M.309, Q.477, F.481, T.487 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.307, A:M.309, A:Q.477, A:T.487, A:T.487 EDO.10: 6 residues within 4Å: Chain A: R.276, E.277 Chain B: F.560, H.564, Y.575, P.576 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Q.486 Hydrogen bonds: B:H.564 EDO.18: 7 residues within 4Å: Chain B: S.323, S.324, V.326, P.327, Y.465, P.466, R.468 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.468 Water bridges: B:S.323, B:C.325, B:R.468, B:R.468 EDO.19: 7 residues within 4Å: Chain A: R.245, Y.266 Chain B: H.46, S.111, A.112, F.115, R.245 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.111, A:Y.266, A:Y.266 EDO.20: 4 residues within 4Å: Chain B: R.245, D.262, S.263, Y.266 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.245, B:R.245, B:D.262 EDO.22: 4 residues within 4Å: Chain B: Q.285, C.288, E.306, T.307 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.285, B:Q.285, B:E.306, B:T.307 Water bridges: B:K.292, B:K.292 EDO.23: 7 residues within 4Å: Chain B: C.288, T.307, V.308, M.309, Q.477, F.481, T.487 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.307, B:M.309, B:Q.477, B:T.487, B:T.487 Water bridges: B:R.488 EDO.24: 8 residues within 4Å: Chain B: F.310, G.311, Y.471, Q.477, T.487, R.488, F.489, T.490 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.311, B:Y.471, B:Q.477, B:T.487, B:R.488, B:F.489 EDO.25: 6 residues within 4Å: Chain A: F.560, H.564, Y.575, P.576 Chain B: R.276, E.277 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.276, A:H.564

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: Q.285, D.289, K.292, D.303, E.306 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.285, A:K.292, A:D.303, A:E.306 Water bridges: A:D.289, A:E.306, A:E.306 GOL.11: 9 residues within 4Å: Chain A: F.310, G.311, Y.471, Q.477, T.487, R.488, F.489, T.490, P.491 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.311, A:Y.471, A:Q.477, A:Q.477, A:F.489, A:T.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rice, K. et al., The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. Nat Commun (2019)

Release Date

2019-08-07

Peptides

Nucleotidyl transferase/aminotransferase, class V: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Nucleotidyl transferase/aminotransferase, class V

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