SMTL ID : 7kto.2 (1 other biounit)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H56A 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 2.13 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: S.291, E.293, N.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.291, A:E.293, A:N.294 EDO.2: 5 residues within 4Å: Chain A: R.72, H.99, E.100, G.103, L.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.72, A:H.99, A:E.100 Water bridges: A:G.103 EDO.3: 2 residues within 4Å: Chain A: R.169, D.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.170 EDO.8: 2 residues within 4Å: Chain B: A.296, E.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.296 EDO.9: 3 residues within 4Å: Chain B: D.162, I.165, K.166 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.169 EDO.10: 1 residues within 4Å: Chain B: R.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.41 EDO.11: 5 residues within 4Å: Chain B: I.17, I.18, I.19, D.52, K.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.17, B:I.19, B:D.52 EDO.15: 3 residues within 4Å: Chain C: S.291, E.293, N.294 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.291, C:N.294 EDO.16: 5 residues within 4Å: Chain C: R.72, H.99, E.100, G.103, L.104 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.72, C:E.100 Water bridges: C:G.103 EDO.17: 2 residues within 4Å: Chain C: R.169, D.170 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.170 EDO.22: 2 residues within 4Å: Chain D: A.296, E.300 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.296 EDO.23: 3 residues within 4Å: Chain D: D.162, I.165, K.166 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.169 EDO.24: 1 residues within 4Å: Chain D: R.41 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.41 EDO.25: 5 residues within 4Å: Chain D: I.17, I.18, I.19, D.52, K.88 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.17, D:I.19, D:D.52

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

PEG.4: 6 residues within 4Å: Chain A: E.203, D.204, A.205, N.256, K.257, F.260 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:E.203, A:A.205, A:K.257 Water bridges: A:E.203, D:D.185 PEG.13: 13 residues within 4Å: Chain A: Y.123 Chain B: V.57, G.58, T.59, S.63, G.92, A.93, G.94, L.117, S.118, V.119, Y.122 Ligands: 3VN.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.59, B:S.63, B:A.93, B:G.94, B:G.94, B:L.117, B:V.119, B:Y.122 Water bridges: B:T.59 PEG.18: 6 residues within 4Å: Chain C: E.203, D.204, A.205, N.256, K.257, F.260 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.203, C:A.205, C:K.257 Water bridges: C:E.203 PEG.27: 13 residues within 4Å: Chain C: Y.123 Chain D: V.57, G.58, T.59, S.63, G.92, A.93, G.94, L.117, S.118, V.119, Y.122 Ligands: 3VN.21 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.63, D:A.93, D:G.94, D:G.94, D:L.117, D:V.119, C:Y.123 Water bridges: D:T.59

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

ACT.5: 6 residues within 4Å: Chain A: Y.149, R.154, K.178, G.202, F.260, N.264 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.264 Water bridges: A:G.202 Salt bridges: A:R.154 ACT.14: 6 residues within 4Å: Chain B: Y.149, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.264 Salt bridges: B:R.154 ACT.19: 6 residues within 4Å: Chain C: Y.149, R.154, K.178, G.202, F.260, N.264 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.264 Hydrogen bonds: C:Y.149 Water bridges: C:G.202 Salt bridges: C:R.154 ACT.28: 6 residues within 4Å: Chain D: Y.149, R.154, K.178, G.202, F.260, N.264 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.264 Salt bridges: D:R.154

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: L.274, E.299 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.274, A:E.299 MG.20: 2 residues within 4Å: Chain C: L.274, E.299 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:L.274, C:E.299

2 x 3VN: (2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid(Non-covalent)

3VN.7: 14 residues within 4Å: Chain A: S.63, A.64, L.66, H.71, N.96, E.100, Y.122 Chain B: S.63, A.64, H.71, N.96, E.100, Y.122 Ligands: PEG.13 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.71, A:N.96, A:N.96, A:N.96, A:Y.122, B:N.96, B:N.96, B:E.100 3VN.21: 14 residues within 4Å: Chain C: S.63, A.64, L.66, H.71, N.96, E.100, Y.122 Chain D: S.63, A.64, H.71, N.96, E.100, Y.122 Ligands: PEG.27 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:H.71, C:N.96, C:N.96, C:N.96, D:N.96, D:N.96, D:E.100, D:Y.122

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

PGE.12: 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 PGE.26: 6 residues within 4Å: Chain D: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saran, S. et al., ALLOSTERIC SITE RESIDUE 'H56' CAPS THE INHIBITOR AT THE TIGHT DIMER INTERFACE FOR TRANSMITTING THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS. To Be Published

Release Date

2021-12-01

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

4-hydroxy-tetrahydrodipicolinate synthase

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