SMTL ID : 8x3z.1

ThDP-dependent HKA synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: R.88, H.90, G.206, Q.207, G.208, T.230, Q.232, G.272, S.273, S.274, A.279, D.297, F.298, D.299, V.302, G.315, D.316, I.317, T.318, H.401 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:H.90, A:Q.207, A:Q.207, A:G.208, A:T.230, A:T.230, A:S.274, A:F.298, A:D.299, A:D.316, A:I.317 Water bridges: A:R.88, A:R.88, A:Q.232 Salt bridges: A:R.88, A:H.401, A:H.401 ADP.3: 20 residues within 4Å: Chain B: R.88, H.90, G.206, Q.207, G.208, T.230, Q.232, G.272, S.273, S.274, A.279, D.297, F.298, D.299, V.302, G.315, D.316, I.317, T.318, H.401 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:H.90, B:Q.207, B:Q.207, B:G.208, B:T.230, B:T.230, B:S.274, B:F.298, B:D.299, B:D.316, B:I.317 Water bridges: B:R.88, B:L.275, B:L.275 Salt bridges: B:R.88, B:H.401, B:H.401 pi-Stacking: B:F.298, B:F.298

1 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 27 residues within 4Å: Chain A: I.22, P.23, A.24, E.48, C.71, P.74, G.75, N.78, Q.111 Chain B: I.377, G.378, E.379, F.380, G.403, A.404, M.405, G.429, D.430, G.431, C.432, M.435, M.455, N.457, R.459, L.460, G.461 Ligands: MG.4 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.460, A:I.22, A:P.74 Hydrogen bonds: B:E.379, B:G.403, B:M.405, B:G.429, B:D.430, B:G.431, B:C.432, B:G.461 Water bridges: A:E.48

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain B: D.430, M.455, N.457, R.459 Ligands: TPP.2 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.430, B:D.430, B:R.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, J.H. et al., ThDP-dependent HKA synthase. To Be Published

Release Date

2024-11-20

Peptides

CsmA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CsmA