SMTL ID : 1rzm.1

Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) from Thermotoga maritima complexed with Cd2+, PEP and E4P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 6 residues within 4Å: Chain A: C.102, H.272, E.298, D.309 Ligands: PEP.4, E4P.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.102, A:H.272, A:E.298, A:D.309 CD.2: 6 residues within 4Å: Chain B: C.102, H.272, E.298, D.309, Q.312 Ligands: E4P.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.102, B:H.272, B:E.298, B:D.309 CD.3: 2 residues within 4Å: Chain B: H.115, E.119 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.115, B:E.119, B:E.119 CD.8: 6 residues within 4Å: Chain C: C.102, H.272, E.298, D.309 Ligands: PEP.11, E4P.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.102, C:H.272, C:E.298, C:D.309 CD.9: 6 residues within 4Å: Chain D: C.102, H.272, E.298, D.309, Q.312 Ligands: E4P.14 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.102, D:H.272, D:E.298, D:D.309 CD.10: 2 residues within 4Å: Chain D: H.115, E.119 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.115, D:E.119, D:E.119

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.4: 12 residues within 4Å: Chain A: R.126, K.131, P.132, Q.182, G.184, A.185, R.186, K.207, R.237, H.272 Ligands: CD.1, E4P.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.132 Hydrogen bonds: A:A.185 Water bridges: A:E.164, A:R.186, A:R.186, A:R.186 Salt bridges: A:R.126, A:K.131, A:R.186, A:K.207, A:K.207, A:R.237, A:H.272, A:H.272 PEP.5: 12 residues within 4Å: Chain B: R.126, K.131, P.132, E.164, Q.182, G.184, A.185, R.186, K.207, R.237, H.272 Ligands: E4P.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.132 Hydrogen bonds: B:A.185, B:R.186 Water bridges: B:E.164, B:R.186 Salt bridges: B:R.126, B:K.131, B:K.207, B:K.207, B:R.237, B:H.272, B:H.272 PEP.11: 12 residues within 4Å: Chain C: R.126, K.131, P.132, Q.182, G.184, A.185, R.186, K.207, R.237, H.272 Ligands: CD.8, E4P.13 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:P.132 Hydrogen bonds: C:A.185 Water bridges: C:R.186, C:R.186, C:R.186 Salt bridges: C:R.126, C:K.131, C:R.186, C:K.207, C:K.207, C:R.237, C:H.272, C:H.272 PEP.12: 12 residues within 4Å: Chain D: R.126, K.131, P.132, E.164, Q.182, G.184, A.185, R.186, K.207, R.237, H.272 Ligands: E4P.14 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:P.132 Hydrogen bonds: D:A.185, D:R.186 Water bridges: D:R.186 Salt bridges: D:R.126, D:K.131, D:K.207, D:K.207, D:R.237, D:H.272, D:H.272

4 x E4P: ERYTHOSE-4-PHOSPHATE(Non-covalent)

E4P.6: 10 residues within 4Å: Chain A: C.102, K.131, P.132, R.133, T.134, R.186, S.308, D.309 Ligands: CD.1, PEP.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.134, A:T.134, A:S.308, A:S.308 Water bridges: A:S.135, A:R.186, A:R.247 Salt bridges: A:R.133 E4P.7: 11 residues within 4Å: Chain B: C.102, K.131, P.132, R.133, T.134, R.186, R.247, S.308, D.309 Ligands: CD.2, PEP.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.131, B:T.134, B:T.134, B:R.186, B:R.186, B:R.247, B:S.308, B:S.308 Water bridges: B:S.135, B:S.138 Salt bridges: B:R.133 E4P.13: 10 residues within 4Å: Chain C: C.102, K.131, P.132, R.133, T.134, R.186, S.308, D.309 Ligands: CD.8, PEP.11 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.134, C:T.134, C:S.308, C:S.308 Water bridges: C:S.135, C:R.186, C:R.247 Salt bridges: C:R.133 E4P.14: 11 residues within 4Å: Chain D: C.102, K.131, P.132, R.133, T.134, R.186, R.247, S.308, D.309 Ligands: CD.9, PEP.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.131, D:T.134, D:R.186, D:R.186, D:R.247, D:S.308, D:S.308 Water bridges: D:S.135, D:S.138 Salt bridges: D:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shumilin, I.A. et al., Crystal Structure of the Reaction Complex of 3-Deoxy-d-arabino-heptulosonate-7-phosphate Synthase from Thermotoga maritima Refines the Catalytic Mechanism and Indicates a New Mechanism of Allosteric Regulation. J.Mol.Biol. (2004)

Release Date

2004-08-10

Peptides

Phospho-2-dehydro-3-deoxyheptonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Phospho-2-dehydro-3-deoxyheptonate aldolase

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