SMTL ID : 5huc.1

DAHP synthase from Corynebacterium glutamicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: C.97, H.379, E.421, D.451 Ligands: PEP.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.97, A:H.379, A:E.421, A:E.421, A:D.451 MN.9: 5 residues within 4Å: Chain B: C.97, H.379, E.421, D.451 Ligands: PEP.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.97, B:H.379, B:E.421, B:E.421, B:D.451 MN.17: 5 residues within 4Å: Chain C: C.97, H.379, E.421, D.451 Ligands: PEP.18 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.97, C:H.379, C:E.421, C:E.421, C:D.451 MN.25: 5 residues within 4Å: Chain D: C.97, H.379, E.421, D.451 Ligands: PEP.26 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.97, D:H.379, D:E.421, D:E.421, D:D.451

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 13 residues within 4Å: Chain A: R.136, K.143, E.258, W.290, G.292, E.293, R.294, K.316, R.347, D.376, H.379, D.451 Ligands: MN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.258 Hydrogen bonds: A:E.293, A:D.376 Water bridges: A:Q.140, A:R.294, A:R.294 Salt bridges: A:R.136, A:K.143, A:R.294, A:K.316, A:K.316, A:R.347, A:H.379, A:H.379 PEP.10: 13 residues within 4Å: Chain B: R.136, K.143, E.258, W.290, G.292, E.293, R.294, K.316, R.347, D.376, H.379, D.451 Ligands: MN.9 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.258 Hydrogen bonds: B:E.293, B:D.376 Water bridges: B:Q.140, B:R.294, B:R.294 Salt bridges: B:R.136, B:K.143, B:R.294, B:K.316, B:K.316, B:R.347, B:H.379, B:H.379 PEP.18: 13 residues within 4Å: Chain C: R.136, K.143, E.258, W.290, G.292, E.293, R.294, K.316, R.347, D.376, H.379, D.451 Ligands: MN.17 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:E.258 Hydrogen bonds: C:E.293 Water bridges: C:Q.140, C:R.294, C:R.294 Salt bridges: C:R.136, C:K.143, C:R.294, C:K.316, C:K.316, C:R.347, C:H.379, C:H.379 PEP.26: 13 residues within 4Å: Chain D: R.136, K.143, E.258, W.290, G.292, E.293, R.294, K.316, R.347, D.376, H.379, D.451 Ligands: MN.25 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:E.258 Hydrogen bonds: D:E.293 Water bridges: D:Q.140, D:R.294, D:R.294 Salt bridges: D:R.136, D:K.143, D:R.294, D:K.316, D:K.316, D:R.347, D:H.379, D:H.379

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 2 residues within 4Å: Chain A: R.409, A.410 No protein-ligand interaction detected (PLIP) MPD.4: 3 residues within 4Å: Chain A: R.181, N.185 Chain B: I.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.185, A:N.185 MPD.5: 6 residues within 4Å: Chain A: E.73, R.194, T.197, D.252, I.253, Y.254 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.73, A:D.252, A:Y.254 Hydrogen bonds: A:D.252, A:I.253, A:I.253 MPD.11: 2 residues within 4Å: Chain B: R.409, A.410 No protein-ligand interaction detected (PLIP) MPD.12: 3 residues within 4Å: Chain A: I.180 Chain B: R.181, N.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.185, B:N.185 MPD.13: 6 residues within 4Å: Chain B: E.73, R.194, T.197, D.252, I.253, Y.254 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.73, B:D.252, B:Y.254 Hydrogen bonds: B:D.252, B:I.253, B:I.253 MPD.19: 2 residues within 4Å: Chain C: R.409, A.410 No protein-ligand interaction detected (PLIP) MPD.20: 3 residues within 4Å: Chain C: R.181, N.185 Chain D: I.180 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.185, C:N.185 MPD.21: 6 residues within 4Å: Chain C: E.73, R.194, T.197, D.252, I.253, Y.254 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:E.73, C:D.252, C:Y.254 Hydrogen bonds: C:T.197, C:D.252, C:I.253, C:I.253 MPD.27: 2 residues within 4Å: Chain D: R.409, A.410 No protein-ligand interaction detected (PLIP) MPD.28: 3 residues within 4Å: Chain C: I.180 Chain D: R.181, N.185 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.185, D:N.185 MPD.29: 6 residues within 4Å: Chain D: E.73, R.194, T.197, D.252, I.253, Y.254 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:E.73, D:D.252, D:Y.254 Hydrogen bonds: D:T.197, D:D.252, D:I.253, D:I.253

4 x TRP: TRYPTOPHAN(Non-covalent)

TRP.6: 12 residues within 4Å: Chain A: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 Chain C: C.241 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:A.120, A:V.121, A:L.207 Hydrogen bonds: A:A.202, A:S.247, W.6, W.6 Salt bridges: A:K.133 pi-Cation interactions: A:K.133 TRP.14: 12 residues within 4Å: Chain B: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 Chain D: C.241 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:A.120, B:V.121, B:L.207 Hydrogen bonds: B:A.202, B:S.247, W.14, W.14 Salt bridges: B:K.133 pi-Cation interactions: B:K.133 TRP.22: 12 residues within 4Å: Chain A: C.241 Chain C: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 9 PLIP interactions: 7 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:A.120, C:V.121, C:L.207 Hydrogen bonds: C:A.202, C:S.247, W.22, W.22 Salt bridges: C:K.133 pi-Cation interactions: C:K.133 TRP.30: 12 residues within 4Å: Chain B: C.241 Chain D: L.117, A.120, V.121, T.124, K.133, A.202, L.207, S.247, L.248, A.250, A.251 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:A.120, D:V.121, D:L.207 Hydrogen bonds: D:A.202, D:S.247, W.30, W.30 Salt bridges: D:K.133 pi-Cation interactions: D:K.133

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 5 residues within 4Å: Chain A: S.307, P.335, N.336, E.338, R.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.336 Salt bridges: A:R.341 PO4.8: 4 residues within 4Å: Chain A: I.40, R.42, A.44, V.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:A.44 PO4.15: 5 residues within 4Å: Chain B: S.307, P.335, N.336, E.338, R.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.336 Salt bridges: B:R.341 PO4.16: 4 residues within 4Å: Chain B: I.40, R.42, A.44, V.262 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.42, B:R.42, B:A.44 PO4.23: 5 residues within 4Å: Chain C: S.307, P.335, N.336, E.338, R.341 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.336 Salt bridges: C:R.341 PO4.24: 4 residues within 4Å: Chain C: I.40, R.42, A.44, V.262 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.42, C:R.42, C:A.44 PO4.31: 5 residues within 4Å: Chain D: S.307, P.335, N.336, E.338, R.341 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.336 Salt bridges: D:R.341 PO4.32: 4 residues within 4Å: Chain D: I.40, R.42, A.44, V.262 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.42, D:R.42, D:A.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burschowsky, D. et al., Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp. Biochemistry (2018)

Release Date

2017-08-02

Peptides

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase

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