SMTL ID : 7kr7.2 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant with pyruvate bound in the active site and L-lysine at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 8 residues within 4Å: Chain A: S.63, A.64, L.66, H.71, Y.122 Chain B: N.96, E.100 Ligands: LYS.10 11 PLIP interactions: 5 interactions with chain A, 3 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: A:H.71, K.10, K.10, B:N.96, B:E.100 Water bridges: A:S.63, A:G.94, A:Y.122, A:Y.122, B:Y.122 Salt bridges: K.1 LYS.10: 8 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, H.71, Y.122 Ligands: LYS.1 9 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: A:N.96, A:N.96, A:E.100, B:H.71, B:Y.122, K.1, K.1, K.10 Salt bridges: K.10

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

PGE.2: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:Q.129, A:S.160 PGE.12: 6 residues within 4Å: Chain B: Q.129, Y.132, S.160, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.160, B:S.160, B:K.166 Water bridges: B:Q.129

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

EDO.3: 3 residues within 4Å: Chain A: T.67, R.284 Chain B: H.99 No protein-ligand interaction detected (PLIP) EDO.4: 7 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.202, A:N.264 Water bridges: A:R.154 EDO.5: 2 residues within 4Å: Chain A: Y.273, L.274 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.276 EDO.6: 3 residues within 4Å: Chain A: Y.273, L.281, F.295 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.273, A:L.281, A:S.289 EDO.13: 4 residues within 4Å: Chain B: E.251, N.254, K.304, Y.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.254, B:K.304 EDO.14: 6 residues within 4Å: Chain B: F.29, K.30, D.35, S.38, I.278, E.279 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.29, B:D.35, B:S.38, B:L.277, B:E.279 Water bridges: B:F.29

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

ACT.7: 3 residues within 4Å: Chain A: P.195, G.214, K.216 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.195 Hydrogen bonds: A:M.197 Salt bridges: A:K.216 ACT.15: 3 residues within 4Å: Chain B: K.15, F.168, R.196 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.15, B:R.196 ACT.16: 6 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, F.260, N.264 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.59, B:N.264 Hydrogen bonds: B:N.264 Salt bridges: B:R.154

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

PEG.8: 3 residues within 4Å: Chain A: H.99 Chain B: T.67, R.284 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.284, B:R.284

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: C.82, K.83, T.85, V.87, K.88, V.89, D.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.82, A:T.85, A:V.89, A:D.114 Water bridges: A:D.114

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS. To Be Published

Release Date

2021-11-24

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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