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

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site and R,R-bislysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

1 x 3VN: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid(Non-covalent)

3VN.1: 18 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, H.71, D.96, E.100, Y.122 Chain B: S.63, A.64, L.66, T.67, H.68, H.71, D.96, E.100, Y.122 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:H.71, A:D.96, A:Y.122, B:H.71, B:D.96, B:E.100 Water bridges: A:E.100, B:E.100, B:Y.122, B:Y.122, B:Y.122, B:Y.122, B:Y.122

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

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: A.232 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain B: D.52 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, H2O.14, H2O.16, H2O.16 MG.7: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP)

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

PGE.5: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.166 Water bridges: A:Q.129 PGE.8: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166

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

EDO.9: 3 residues within 4Å: Chain A: T.67, R.284 Chain B: H.99 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.284, B:H.99 EDO.10: 4 residues within 4Å: Chain B: L.274, A.275, M.302, I.307 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.274 EDO.11: 5 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, Y.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:Y.305 EDO.12: 2 residues within 4Å: Chain B: K.44, E.48 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., A TIGHT DIMER INTERFACE N84 RESIDUE, PLAYS A CRITICAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS. To Be Published

Release Date

2021-11-03

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

4-hydroxy-tetrahydrodipicolinate synthase

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