SMTL ID : 5j6f.1

Crystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: C.126, H.296, E.322, D.333 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.126, A:H.296, A:E.322, A:E.322, A:D.333 MN.5: 4 residues within 4Å: Chain B: C.126, H.296, E.322, D.333 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:C.126, B:H.296, B:E.322, B:E.322, B:D.333 MN.9: 4 residues within 4Å: Chain C: C.126, H.296, E.322, D.333 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.126, C:H.296, C:E.322, C:E.322, C:D.333 MN.13: 4 residues within 4Å: Chain D: C.126, H.296, E.322, D.333 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.126, D:H.296, D:E.322, D:E.322, D:D.333

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: P.156, R.157, T.158, D.162, R.210 Chain C: H.44 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.158, A:T.158, A:T.158, A:D.162, A:R.271 Salt bridges: A:R.157, A:R.210, C:H.44 SO4.3: 6 residues within 4Å: Chain A: G.208, A.209, R.210, K.231, R.261, H.296 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.209, A:R.210 Salt bridges: A:K.231, A:R.261, A:H.296 SO4.6: 5 residues within 4Å: Chain B: G.208, A.209, K.231, R.261, H.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.209 Salt bridges: B:K.231, B:R.261, B:H.296 SO4.7: 5 residues within 4Å: Chain B: R.210, L.234, R.261, R.271, N.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.272 Salt bridges: B:R.210, B:R.261, B:R.271 SO4.10: 6 residues within 4Å: Chain A: H.44 Chain C: P.156, R.157, T.158, D.162, R.210 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.158, C:T.158, C:T.158, C:D.162, C:R.271 Salt bridges: C:R.157, C:R.210, A:H.44 SO4.11: 6 residues within 4Å: Chain C: G.208, A.209, R.210, K.231, R.261, H.296 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.209, C:R.210 Salt bridges: C:K.231, C:R.261, C:H.296 SO4.14: 5 residues within 4Å: Chain D: G.208, A.209, K.231, R.261, H.296 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.209 Salt bridges: D:K.231, D:R.261, D:H.296 SO4.15: 5 residues within 4Å: Chain D: R.210, L.234, R.261, R.271, N.272 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.272 Salt bridges: D:R.210, D:R.261, D:R.271

4 x PRE: PREPHENIC ACID(Non-covalent)

PRE.4: 14 residues within 4Å: Chain A: R.27, I.34, K.38, R.45, Y.46, D.47, R.50, E.51, M.54, F.79, A.82, L.83, Q.86 Chain D: R.10 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:R.50, A:E.51, A:L.83 Hydrogen bonds: A:R.45, A:D.47, A:F.79, A:Q.86 Salt bridges: A:R.27, A:K.38, A:R.50, D:R.10 PRE.8: 13 residues within 4Å: Chain B: R.27, I.34, K.38, R.45, Y.46, D.47, R.50, E.51, M.54, F.79, A.82, Q.86 Chain C: R.10 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:R.50, B:E.51 Hydrogen bonds: B:R.45, B:D.47, B:E.51, B:Q.86 Salt bridges: B:R.27, B:K.38, B:R.50, C:R.10 PRE.12: 14 residues within 4Å: Chain B: R.10 Chain C: R.27, I.34, K.38, R.45, Y.46, D.47, R.50, E.51, M.54, F.79, A.82, L.83, Q.86 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:R.50, C:E.51, C:L.83 Hydrogen bonds: C:R.45, C:D.47, C:F.79, C:Q.86 Salt bridges: C:R.27, C:K.38, C:R.50, B:R.10 PRE.16: 13 residues within 4Å: Chain A: R.10 Chain D: R.27, I.34, K.38, R.45, Y.46, D.47, R.50, E.51, M.54, F.79, A.82, Q.86 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain D Salt bridges: A:R.10, D:R.27, D:K.38, D:R.50 Hydrophobic interactions: D:R.50, D:E.51 Hydrogen bonds: D:R.45, D:D.47, D:E.51, D:Q.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nazmi, A.R. et al., Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate. J. Biol. Chem. (2016)

Release Date

2016-09-07

Peptides

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3