SMTL ID : 7kly.3 (2 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 11 residues within 4Å: Chain A: S.63, A.64, L.66, T.67, H.68, N.71, N.96, Y.122 Chain B: N.96, E.100 Ligands: LYS.12 9 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: K.12, K.12, K.12, A:N.71, B:N.96, B:N.96 Salt bridges: K.1 Water bridges: A:Y.122, B:Y.122 LYS.12: 11 residues within 4Å: Chain A: N.96, E.100 Chain B: S.63, A.64, L.66, T.67, H.68, N.71, N.96, Y.122 Ligands: LYS.1 8 PLIP interactions: 4 Ligand-Ligand interactions, 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: K.1, K.1, K.1, A:N.96, A:E.100, B:N.71, B:Y.122 Salt bridges: K.12

2 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166 PG4.13: 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:K.166 Water bridges: B:Q.129, B:Y.132

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

EDO.3: 3 residues within 4Å: Chain A: K.308, G.309, F.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.309, A:F.310 EDO.4: 4 residues within 4Å: Chain A: Q.37, A.40, R.41, K.44 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: F.168, C.171, E.172, I.174, Y.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.168 Water bridges: A:N.16, A:E.172 EDO.6: 7 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.202, A:N.264 EDO.7: 3 residues within 4Å: Chain A: H.235, F.236, D.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.239 EDO.8: 2 residues within 4Å: Chain A: Y.208, K.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.242 EDO.9: 2 residues within 4Å: Chain A: I.19, M.198 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain B: K.136, Q.140, D.170, C.171, E.172 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.140, B:E.172 Water bridges: B:A.139 EDO.15: 7 residues within 4Å: Chain B: T.59, Y.149, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.202, B:N.264 EDO.16: 5 residues within 4Å: Chain B: C.82, T.85, K.86, V.87, D.114 2 PLIP interactions: 2 interactions with chain B Water bridges: B:C.82, B:T.85 EDO.17: 5 residues within 4Å: Chain B: R.41, K.44, R.45, E.48, F.310 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.41, B:R.45, B:E.48, B:F.310 EDO.18: 2 residues within 4Å: Chain B: H.235, F.236 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.235 EDO.19: 3 residues within 4Å: Chain B: G.84, T.85, K.86 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.86 EDO.20: 3 residues within 4Å: Chain B: R.284, L.285 Ligands: ACT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.285

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

ACT.10: 3 residues within 4Å: Chain A: T.98, H.99 Ligands: EDO.20 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.99 ACT.21: 3 residues within 4Å: Chain B: D.162, D.189, H.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.162 Salt bridges: B:H.193 ACT.22: 4 residues within 4Å: Chain B: A.180, S.181, G.182, E.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.203

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

PGE.11: 4 residues within 4Å: Chain A: R.169, E.194, P.195, R.196 No protein-ligand interaction detected (PLIP) PGE.23: 4 residues within 4Å: Chain B: K.44, I.47, E.48, T.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.44, B:E.48

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.24: 4 residues within 4Å: Chain B: I.17, I.19, M.198, K.216 No protein-ligand interaction detected (PLIP)

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
E

B
F

4-hydroxy-tetrahydrodipicolinate synthase

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