SMTL ID : 4umc.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 2.34 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: PEQ.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:H.270, A:E.304, A:D.324 MN.4: 5 residues within 4Å: Chain B: C.63, H.270, E.304, D.324 Ligands: PEQ.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:H.270, B:E.304, B:D.324 MN.7: 5 residues within 4Å: Chain C: C.63, H.270, E.304, D.324 Ligands: PEQ.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.63, C:H.270, C:E.304, C:D.324 MN.10: 5 residues within 4Å: Chain D: C.63, H.270, E.304, D.324 Ligands: PEQ.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.63, D:H.270, D:E.304, D:D.324

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

PO4.2: 2 residues within 4Å: Chain A: R.101, T.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.102, A:T.102 Salt bridges: A:R.101 PO4.6: 4 residues within 4Å: Chain B: R.101, T.102, T.103, V.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.102, B:T.103 Salt bridges: B:R.101 PO4.9: 2 residues within 4Å: Chain C: R.101, T.102 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.102, C:T.102, C:T.102 Salt bridges: C:R.101 PO4.11: 3 residues within 4Å: Chain D: P.100, R.101, T.102 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.102, D:T.102 Water bridges: D:D.324 Salt bridges: D:R.101

4 x PEQ: L-PHOSPHOLACTATE(Non-covalent)

PEQ.3: 15 residues within 4Å: Chain A: C.63, R.94, Y.96, K.99, P.100, E.145, G.165, A.166, R.167, K.188, R.236, H.270, E.304, D.324 Ligands: MN.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.100 Hydrogen bonds: A:A.166 Water bridges: A:R.94, A:Y.96, A:E.145, A:R.167, A:R.167, A:K.188 Salt bridges: A:R.94, A:K.99, A:R.167, A:K.188, A:K.188, A:R.236, A:H.270, A:H.270 PEQ.5: 14 residues within 4Å: Chain B: C.63, R.94, Y.96, K.99, E.145, G.165, A.166, R.167, K.188, R.236, H.270, E.304, D.324 Ligands: MN.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:A.166 Water bridges: B:R.94, B:R.94, B:R.167, B:R.167 Salt bridges: B:R.94, B:K.99, B:R.167, B:K.188, B:K.188, B:R.236, B:H.270, B:H.270 PEQ.8: 14 residues within 4Å: Chain C: C.63, R.94, Y.96, K.99, E.145, G.165, A.166, R.167, K.188, R.236, H.270, E.304, D.324 Ligands: MN.7 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.166 Water bridges: C:R.94, C:E.145, C:K.188 Salt bridges: C:R.94, C:K.99, C:R.167, C:K.188, C:K.188, C:R.236, C:H.270, C:H.270 PEQ.12: 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.10 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:A.166 Water bridges: D:R.94, D:Y.96, D:R.167, D:K.188 Salt bridges: D:R.94, D:K.99, D:R.167, D:K.188, D:K.188, D:R.236, D:H.270, 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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