SMTL ID : 4uma.1

Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3 deoxy D arabino heptulosonate 7 phosphate synthase the importance of accommodating the active site water

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: C.63, H.270, E.304, D.324 Ligands: GZ3.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:H.270, A:E.304, A:D.324 MN.3: 5 residues within 4Å: Chain B: C.63, H.270, E.304, D.324 Ligands: GZ3.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:H.270, B:E.304, B:D.324 MN.5: 5 residues within 4Å: Chain C: C.63, H.270, E.304, D.324 Ligands: GZ3.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.63, C:H.270, C:E.304, C:D.324 MN.7: 5 residues within 4Å: Chain D: C.63, H.270, E.304, D.324 Ligands: GZ3.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.63, D:H.270, D:E.304, D:D.324

4 x GZ3: (E)-2-METHYL-3-PHOSPHONOACRYLATE(Non-covalent)

GZ3.2: 14 residues within 4Å: Chain A: C.63, R.94, Y.96, K.99, P.100, G.165, A.166, R.167, K.188, R.236, H.270, E.304, D.324 Ligands: MN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.100 Hydrogen bonds: A:A.166, A:R.167, A:R.167, A:K.188, A:R.236 Water bridges: A:R.94, A:R.167 Salt bridges: A:R.94, A:K.99, A:K.188, A:H.270 GZ3.4: 14 residues within 4Å: Chain B: C.63, R.94, Y.96, K.99, P.100, G.165, A.166, R.167, K.188, R.236, H.270, E.304, D.324 Ligands: MN.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.100 Hydrogen bonds: B:A.166, B:R.167, B:R.167, B:K.188, B:K.188, B:R.236 Water bridges: B:R.94, B:E.145, B:E.145, B:R.167, B:R.167 Salt bridges: B:R.94, B:K.99, B:K.188, B:H.270 GZ3.6: 14 residues within 4Å: Chain C: C.63, R.94, Y.96, K.99, P.100, G.165, A.166, R.167, K.188, R.236, H.270, E.304, D.324 Ligands: MN.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:P.100 Hydrogen bonds: C:A.166, C:R.167, C:R.167, C:K.188, C:R.236 Water bridges: C:R.94, C:R.167 Salt bridges: C:R.94, C:K.99, C:K.188, C:H.270 GZ3.8: 13 residues within 4Å: Chain D: C.63, R.94, Y.96, K.99, G.165, A.166, R.167, K.188, R.236, H.270, E.304, D.324 Ligands: MN.7 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:A.166, D:R.167, D:R.167, D:K.188, D:K.188, D:R.236 Water bridges: D:R.94, D:R.167, D:K.188 Salt bridges: D:R.94, D:K.99, D:K.188, D:H.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heyes, L.C. et al., Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water. Bioorg.Chem. (2014)

Release Date

2014-10-08

Peptides

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE

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