SMTL ID : 6pd1.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.104, D.106, E.220 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.104, A:D.106, A:D.106, A:E.220 MG.8: 4 residues within 4Å: Chain B: K.25, E.104, D.106, E.220 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.106, H2O.3

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

SO4.2: 5 residues within 4Å: Chain A: E.49, P.70, A.71, L.504, K.507 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.507 SO4.3: 7 residues within 4Å: Chain A: L.293, F.294, L.296, A.297, P.424, M.425, V.511 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.294, A:L.296, A:M.425 Water bridges: A:V.511 SO4.6: 7 residues within 4Å: Chain A: S.313, G.314, T.315, Y.340, R.343 Chain B: F.489, T.490 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.314, A:T.315, A:T.315, A:T.315, A:Y.340, A:R.343, B:T.490 Salt bridges: A:K.441 SO4.9: 6 residues within 4Å: Chain A: F.489, T.490 Chain B: S.313, G.314, T.315, Y.340 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.314, B:T.315, B:T.315, A:T.490, A:T.490 Salt bridges: B:K.441 SO4.13: 5 residues within 4Å: Chain B: M.1, K.3, A.279, D.282, L.283 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.3

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

EDO.4: 6 residues within 4Å: Chain A: R.122, K.123, N.124, C.147, P.207, A.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.123, A:N.124, A:N.124 Water bridges: A:N.124 EDO.5: 5 residues within 4Å: Chain A: Q.285, C.288, E.306, T.307, F.481 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.306, A:T.307, A:T.307 EDO.7: 6 residues within 4Å: Chain A: M.1, I.118, N.119, S.270, A.271 Chain B: R.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.1, A:A.271 EDO.10: 7 residues within 4Å: Chain B: C.288, T.307, V.308, M.309, Q.477, F.481, T.487 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.307, B:M.309, B:Q.477, B:T.487

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain B: P.255, S.339, Y.340, R.343, T.390, Y.575, K.578, R.586 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.339, B:S.339, B:Y.340, B:R.343, B:Y.575, B:Y.575, B:K.578, B:R.586, B:R.586

1 x NI: NICKEL (II) ION(Non-covalent)

NI.12: 2 residues within 4Å: Chain B: H.620, H.622 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.620, B:H.622

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
A

B
C

Nucleotidyl transferase/aminotransferase, class V

Related Entries With Identical Sequence