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

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

PG4.1: 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:K.166 PG4.15: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.129, B:K.166 Water bridges: B:K.166

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: N.241 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: D.250, E.251, Y.253, N.254, K.304 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.250, H2O.5 MG.4: 1 residues within 4Å: Chain A: D.239 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.239, H2O.3, H2O.3, H2O.4 MG.16: 3 residues within 4Å: Chain B: S.63, A.64, Y.122 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain B: E.100 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.100, H2O.2, H2O.5

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

EDO.5: 4 residues within 4Å: Chain A: K.44, I.47, E.48, T.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.44, A:E.48, A:E.48, A:T.81 EDO.6: 4 residues within 4Å: Chain A: A.180, S.181, G.182, E.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.182, A:E.203 EDO.7: 3 residues within 4Å: Chain A: P.152, G.156, C.157 No protein-ligand interaction detected (PLIP) EDO.18: 6 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, K.304, Y.305 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:K.304, B:Y.305, B:Y.305 Water bridges: B:N.254 EDO.19: 3 residues within 4Å: Chain A: E.262, S.291 Chain B: Q.129 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:T.127, A:E.262 Hydrogen bonds: A:S.291 EDO.20: 5 residues within 4Å: Chain B: I.18, I.19, D.52, A.53, K.88 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.17, B:I.19, B:D.52 Water bridges: B:D.52 EDO.21: 2 residues within 4Å: Chain B: I.19, K.216 No protein-ligand interaction detected (PLIP) EDO.22: 5 residues within 4Å: Chain B: H.68, E.100, G.103, L.104, F.107 No protein-ligand interaction detected (PLIP)

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

PGE.8: 8 residues within 4Å: Chain A: Y.149, R.154, K.178, F.260, E.262, S.263, N.264 Chain B: K.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.154, A:F.260, A:N.264, A:N.264 PGE.23: 4 residues within 4Å: Chain B: V.79, K.83, G.112, D.114 No protein-ligand interaction detected (PLIP)

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

ACT.9: 6 residues within 4Å: Chain A: L.211, G.214, G.215, K.216, A.237, Y.242 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.216 Salt bridges: A:K.216 ACT.10: 2 residues within 4Å: Chain A: H.99 Chain B: R.284 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.284, A:H.99 ACT.11: 4 residues within 4Å: Chain A: I.19, G.20, D.52, L.238 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.52 ACT.24: 5 residues within 4Å: Chain B: Y.149, R.154, K.178, F.260, N.264 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.260, B:N.264 Hydrogen bonds: B:N.264 Salt bridges: B:R.154

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

PEG.12: 3 residues within 4Å: Chain A: I.47, E.48, G.50 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.86 PEG.13: 4 residues within 4Å: Chain A: I.19, M.198, K.216, L.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.238 PEG.25: 3 residues within 4Å: Chain B: P.126, T.127, Q.128 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.128, B:Q.128 Water bridges: B:Q.129, B:Q.129, B:E.158

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain A: D.162, D.189, H.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.162, A:H.193 Water bridges: A:D.162 GOL.26: 4 residues within 4Å: Chain B: T.161, D.162, D.189, H.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.189 Water bridges: B:T.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME. 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
C

4-hydroxy-tetrahydrodipicolinate synthase

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