SMTL ID : 7kkg.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.9: 6 residues within 4Å: Chain B: H.8, H.9, H.10, G.11, R.169, R.196 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.8, H2O.23 MG.10: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: D.189, H.193 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.189, H2O.25, H2O.25 MG.15: 5 residues within 4Å: Chain C: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.23: 6 residues within 4Å: Chain D: H.8, H.9, H.10, G.11, R.169, R.196 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.8, H2O.53 MG.24: 5 residues within 4Å: Chain D: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain D: D.189, H.193 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.189, H2O.55, H2O.55

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 3 residues within 4Å: Chain A: E.300, K.303, K.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.300, A:K.304 PG4.12: 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:T.163, B:K.166 Water bridges: B:Q.129, B:S.160 PG4.17: 3 residues within 4Å: Chain C: E.300, K.303, K.304 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.304 PG4.26: 6 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.166 Water bridges: D:Q.129, D:S.160

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

PEG.4: 6 residues within 4Å: Chain A: G.32, K.33, T.67, R.284 Chain B: H.99 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.33 PEG.13: 3 residues within 4Å: Chain A: H.99 Chain B: T.67, R.284 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.99 PEG.18: 6 residues within 4Å: Chain C: G.32, K.33, T.67, R.284 Chain D: H.99 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.33 PEG.27: 3 residues within 4Å: Chain C: H.99 Chain D: T.67, R.284 No protein-ligand interaction detected (PLIP)

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

PGE.5: 4 residues within 4Å: Chain A: Y.273, P.290, K.292, F.295 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.281 PGE.19: 4 residues within 4Å: Chain C: Y.273, P.290, K.292, F.295 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.281

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

EDO.6: 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.7: 5 residues within 4Å: Chain A: K.33, T.67, E.70, R.284 Ligands: PEG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.33, A:K.33, A:R.284 EDO.20: 4 residues within 4Å: Chain C: Q.140, D.170, C.171, E.172 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.140, C:E.172 Water bridges: C:A.139 EDO.21: 5 residues within 4Å: Chain C: K.33, T.67, E.70, R.284 Ligands: PEG.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.33, C:K.33, C:R.284

4 x LYS: LYSINE(Non-covalent)

LYS.8: 11 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, H.71, D.96, Y.122 Chain B: D.96, E.100 Ligands: LYS.14 8 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: A:H.71, A:Y.122, B:E.100, K.14, K.14, K.14 Water bridges: A:S.63 Salt bridges: K.8 LYS.14: 11 residues within 4Å: Chain A: D.96, E.100 Chain B: S.63, A.64, L.66, T.67, H.68, H.71, D.96, Y.122 Ligands: LYS.8 9 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, 4 Ligand-Ligand interactions Hydrogen bonds: A:E.100, B:H.71, K.8, K.8, K.8 Water bridges: A:Y.122, B:S.63, B:S.63 Salt bridges: K.14 LYS.22: 11 residues within 4Å: Chain C: S.63, A.64, L.66, T.67, H.68, H.71, D.96, Y.122 Chain D: D.96, E.100 Ligands: LYS.28 9 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: K.28, K.28, K.28, D:E.100, C:H.71 Salt bridges: K.22 Water bridges: D:D.96, C:S.63, C:S.63 LYS.28: 11 residues within 4Å: Chain C: D.96, E.100 Chain D: S.63, A.64, L.66, T.67, H.68, H.71, D.96, Y.122 Ligands: LYS.22 9 PLIP interactions: 4 interactions with chain D, 4 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: D:H.71, D:Y.122, K.22, K.22, K.22, C:E.100 Water bridges: D:S.63, D:D.96 Salt bridges: K.28

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
A

D
D

4-hydroxy-tetrahydrodipicolinate synthase

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