SMTL ID : 7kz2.2 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site in C2221 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 9 residues within 4Å: Chain A: S.63, A.64, L.66, H.68, H.71, F.122 Chain B: N.96, E.100 Ligands: LYS.11 7 PLIP interactions: 2 interactions with chain A, 3 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: A:H.71, K.11, K.11, B:N.96, B:E.100 Water bridges: A:S.63 Salt bridges: K.1 LYS.11: 9 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, H.68, H.71, F.122 Ligands: LYS.1 8 PLIP interactions: 2 interactions with chain B, 4 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: B:A.64, B:H.71, K.1, K.11, A:N.96, A:E.100 Water bridges: K.11 Salt bridges: K.11

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: G.32, K.33, T.67 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain B: K.109, E.110, G.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.109 PEG.13: 3 residues within 4Å: Chain B: P.126, T.127, Q.128 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.126, B:Q.128, B:Q.128 Water bridges: B:E.158, B:E.158

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

EDO.3: 2 residues within 4Å: Chain A: G.50, H.235 No protein-ligand interaction detected (PLIP) EDO.4: 7 residues within 4Å: Chain A: L.211, G.215, K.216, A.237, L.238, E.240, Y.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.211, A:K.216, A:Y.242 EDO.5: 4 residues within 4Å: Chain A: T.67, H.68, E.69, E.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.67, A:H.68, A:E.69 EDO.6: 5 residues within 4Å: Chain A: R.41, K.44, R.45, E.48, F.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.45 EDO.14: 6 residues within 4Å: Chain B: A.139, Q.140, D.170, C.171, E.172, N.173 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.172, B:N.173, B:N.173, B:N.173 EDO.15: 2 residues within 4Å: Chain B: E.80, K.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.83, B:K.83 EDO.16: 7 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.215, B:K.216 Water bridges: B:K.216, B:Y.242 EDO.17: 3 residues within 4Å: Chain B: A.275, I.307, G.309 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain B: C.82, T.85, K.86, V.87 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.86 Water bridges: B:T.85, B:T.85

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.7: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.4, H2O.6 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 5 residues within 4Å: Chain A: K.30, V.34, D.35, E.36, Q.37 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.37 Hydrogen bonds: A:D.35, A:E.36 Salt bridges: A:K.30

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PGE.20: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.162, B:K.166 Water bridges: B:S.160, B:K.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS. To Be Published

Release Date

2021-12-15

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

4-hydroxy-tetrahydrodipicolinate synthase

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