SMTL ID : 7kk1.2 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84A mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 9 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, H.71, Y.122 Chain B: E.100 Ligands: LYS.18 7 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.100, A:H.71 Water bridges: B:Y.122, A:S.63, A:E.100, A:E.100 Salt bridges: K.1 LYS.18: 9 residues within 4Å: Chain A: E.100 Chain B: S.63, A.64, L.66, T.67, H.68, H.71, Y.122 Ligands: LYS.1 8 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: B:A.64, B:H.71, B:Y.122, A:E.100, K.18 Water bridges: B:S.63, K.18 Salt bridges: K.18

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

MG.2: 5 residues within 4Å: Chain A: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.3: 8 residues within 4Å: Chain A: P.121, Y.122, Y.123, N.124, K.125, P.126, T.155, C.157 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:P.121, A:T.155 MG.4: 1 residues within 4Å: Chain A: D.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.239, H2O.4, H2O.5 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain B: A.93, G.94, L.117, S.118, V.119 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain B: S.291, K.292, E.293 No protein-ligand interaction detected (PLIP)

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

EDO.7: 2 residues within 4Å: Chain A: H.99 Chain B: T.67 No protein-ligand interaction detected (PLIP) EDO.8: 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.9: 3 residues within 4Å: Chain A: T.161, D.189, H.193 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.193 Water bridges: A:T.161, A:T.161, A:T.161 EDO.10: 5 residues within 4Å: Chain A: S.212, G.214, E.240, Y.242 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.212, A:E.240 EDO.11: 9 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, L.238, E.240, Y.242 Ligands: EDO.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.211, A:K.216, A:E.240, A:E.240, A:Y.242 EDO.12: 3 residues within 4Å: Chain A: I.47, T.85, K.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.47 Water bridges: A:G.50 EDO.13: 5 residues within 4Å: Chain A: V.34, E.36, E.69, E.70, T.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.36, A:T.73, A:T.73 EDO.21: 8 residues within 4Å: Chain B: L.211, G.214, G.215, K.216, A.237, L.238, Y.242 Ligands: ACT.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.215, B:K.216, B:Y.242 EDO.22: 2 residues within 4Å: Chain B: M.198, K.216 No protein-ligand interaction detected (PLIP) EDO.23: 6 residues within 4Å: Chain B: C.82, T.85, K.86, V.87, K.88, D.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.82 Water bridges: B:G.84

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

ACT.14: 4 residues within 4Å: Chain A: I.17, I.19, M.198, K.216 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.216 ACT.15: 6 residues within 4Å: Chain A: T.59, Y.149, V.151, R.154, K.178, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.264 Salt bridges: A:R.154 ACT.16: 3 residues within 4Å: Chain A: K.83, G.84, T.85 No protein-ligand interaction detected (PLIP) ACT.24: 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.25: 5 residues within 4Å: Chain B: Y.149, V.151, R.154, F.260, N.264 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.260, B:N.264 Salt bridges: B:R.154 ACT.26: 4 residues within 4Å: Chain B: S.212, G.214, Y.242 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.212

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

PGE.17: 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 PGE.27: 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

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

PEG.28: 3 residues within 4Å: Chain A: T.67, R.284 Chain B: H.99 1 PLIP interactions: 1 interactions with chain B Water bridges: B: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
C

4-hydroxy-tetrahydrodipicolinate synthase

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