SMTL ID : 7kr8.1 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A mutant with pyruvate bound in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Q.140, D.170, C.171, E.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.140, A:E.172 Water bridges: A:A.139 EDO.2: 3 residues within 4Å: Chain A: H.99 Chain B: T.67, R.284 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.284 EDO.7: 3 residues within 4Å: Chain B: S.212, E.240, Y.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.240, B:Y.242 Water bridges: B:K.216

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

PGE.3: 7 residues within 4Å: Chain A: Q.128, Q.129, Y.132, S.160, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.132, A:S.160, A:S.160, A:K.166 PGE.8: 4 residues within 4Å: Chain B: Q.129, Y.132, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166

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

ACT.4: 6 residues within 4Å: Chain A: V.151, R.154, K.178, G.202, F.260, N.264 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.260 Hydrogen bonds: A:N.264 Water bridges: A:R.154 Salt bridges: A:R.154 ACT.5: 3 residues within 4Å: Chain A: I.17, M.198, K.216 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.216 ACT.9: 2 residues within 4Å: Chain B: Y.273, L.274 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.273 Water bridges: B:Y.273, B:G.276

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain B: N.183, I.184, D.185 No protein-ligand interaction detected (PLIP)

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

PEG.10: 2 residues within 4Å: Chain B: I.19, K.216 No protein-ligand interaction detected (PLIP) PEG.11: 5 residues within 4Å: Chain B: V.34, E.36, E.69, E.70, T.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.36, B:E.36 Water bridges: B:V.34

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
A

B
B

4-hydroxy-tetrahydrodipicolinate synthase

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