SMTL ID : 7kkt.2 (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, 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 Ligands: MG.10 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:H.71, B:E.100, A:H.71, A:D.96, A:D.96, A:Y.122 Water bridges: B:S.63, B:G.94, B:Y.122, B:Y.122, A:E.100, A:Y.122

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

PG4.2: 6 residues within 4Å: Chain A: Q.128, 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

9 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.12, R.196 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.12 MG.4: 2 residues within 4Å: Chain A: S.263 Chain B: K.125 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.263, H2O.5 MG.5: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: S.95, E.100, Y.122 Ligands: 3VN.1 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.95, B:E.100, H2O.7 MG.11: 1 residues within 4Å: Chain B: I.307 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.307, H2O.18 MG.12: 3 residues within 4Å: Chain B: K.15, N.16, E.172 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.172, H2O.12 MG.13: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain B: K.106, E.110 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.110, H2O.12 MG.15: 1 residues within 4Å: Chain B: V.79 No protein-ligand interaction detected (PLIP)

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

ACT.6: 4 residues within 4Å: Chain A: T.67, E.70, R.284 Chain B: H.99 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.67 Salt bridges: A:K.33, A:R.284, B:H.99 ACT.7: 6 residues within 4Å: Chain A: T.59, V.151, R.154, K.178, F.260, N.264 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:N.264 Salt bridges: A:R.154 ACT.18: 2 residues within 4Å: Chain A: L.285 Chain B: H.99 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:H.99, A:L.285 Hydrophobic interactions: A:L.285

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

EDO.8: 4 residues within 4Å: Chain A: L.274, E.299, M.302, K.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.303, A:K.303 EDO.9: 5 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, Y.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.253, A:N.254 EDO.19: 8 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.214, B:K.216, B:L.238, B:E.240 EDO.20: 6 residues within 4Å: Chain B: Y.149, R.154, K.178, G.202, F.260, N.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.154, B:R.154, B:G.202, B:N.264 EDO.21: 6 residues within 4Å: Chain B: K.136, Q.140, D.170, C.171, E.172 Ligands: EDO.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.140, B:E.172 Water bridges: B:A.139 EDO.22: 5 residues within 4Å: Chain B: A.139, Q.140, V.142, N.173 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.173 Water bridges: B:A.139, B:N.173

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

PEG.16: 5 residues within 4Å: Chain B: Q.129, Y.132, D.162, T.163, K.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.166 Water bridges: B:Q.129, B:Q.129, B:S.160, B:S.160 PEG.17: 4 residues within 4Å: Chain A: H.99 Chain B: G.32, K.33, R.284 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.33 Water bridges: A:H.99, A:H.99

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
B

B
E

4-hydroxy-tetrahydrodipicolinate synthase

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