SMTL ID : 5czs.1

Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu98Ala variant regulated

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 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: PEP.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.63, A:H.270, A:E.304, A:D.324, H2O.2 MN.6: 5 residues within 4Å: Chain B: C.63, H.270, E.304, D.324 Ligands: PEP.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:H.270, B:E.304, B:D.324 MN.9: 4 residues within 4Å: Chain C: C.63, H.270, E.304, D.324 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.63, C:H.270, C:E.304, C:D.324, H2O.7 MN.14: 4 residues within 4Å: Chain D: C.63, H.270, E.304, D.324 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.63, D:H.270, D:E.304, D:D.324, H2O.12

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 12 residues within 4Å: Chain A: R.94, Y.96, P.100, G.165, A.166, R.167, K.188, R.236, H.270, M.302, E.304 Ligands: MN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.100 Hydrogen bonds: A:Y.96, A:A.166 Water bridges: A:R.94, A:E.145, A:R.167, A:R.236 Salt bridges: A:R.94, A:R.167, A:K.188, A:K.188, A:R.236, A:H.270, A:H.270 PEP.7: 11 residues within 4Å: Chain B: R.94, Y.96, P.100, E.145, G.165, A.166, R.167, K.188, R.236, H.270 Ligands: MN.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.145, B:A.166, B:D.267 Water bridges: B:R.167 Salt bridges: B:R.94, B:R.167, B:K.188, B:K.188, B:R.236, B:H.270, B:H.270 PEP.10: 8 residues within 4Å: Chain C: R.94, Y.96, P.100, A.166, R.167, K.188, R.236, H.270 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:A.166 Water bridges: C:R.94 Salt bridges: C:R.94, C:R.167, C:K.188, C:K.188, C:R.236, C:H.270, C:H.270 PEP.15: 9 residues within 4Å: Chain D: R.94, Y.96, P.100, A.166, R.167, K.188, R.236, H.270, M.302 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:P.100 Hydrogen bonds: D:Y.96, D:A.166 Water bridges: D:R.94, D:E.145, D:R.167, D:R.236 Salt bridges: D:R.94, D:R.167, D:K.188, D:K.188, D:R.236, D:H.270, D:H.270

4 x PHE: PHENYLALANINE(Non-covalent)

PHE.3: 14 residues within 4Å: Chain A: M.149, P.152, Q.153, A.156, L.177, G.180, L.181, S.182, F.211, S.213, K.216 Chain B: D.8, D.9, I.12 13 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:P.152, A:Q.153, A:L.177, A:F.211, B:I.12 Hydrogen bonds: A:Q.153, A:S.182, A:K.216, B:D.8, B:D.9, F.3 Water bridges: A:D.157, A:C.183 PHE.8: 13 residues within 4Å: Chain A: D.8, D.9 Chain B: M.149, P.152, Q.153, A.156, G.180, L.181, S.182, F.211, S.213, K.216, V.223 11 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: B:P.152, B:Q.153, B:F.211, B:V.223 Hydrogen bonds: B:Q.153, B:S.182, B:K.216, A:D.8, A:D.9, F.8 Water bridges: F.8 PHE.11: 15 residues within 4Å: Chain C: M.149, P.152, Q.153, A.156, L.177, G.180, L.181, S.182, F.211, S.213, K.216, V.223 Chain D: T.7, D.8, D.9 13 PLIP interactions: 3 interactions with chain D, 10 interactions with chain C Hydrogen bonds: D:D.8, D:D.9, D:D.9, C:Q.153, C:S.182, C:K.216 Hydrophobic interactions: C:P.152, C:Q.153, C:L.177, C:F.211, C:F.211, C:V.223 Water bridges: C:D.157 PHE.16: 14 residues within 4Å: Chain C: D.8, D.9 Chain D: M.149, P.152, Q.153, A.156, L.177, G.180, L.181, S.182, F.211, S.213, K.216, V.223 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C, Hydrophobic interactions: D:P.152, D:Q.153, D:L.177, D:F.211, D:F.211, D:V.223 Hydrogen bonds: D:Q.153, D:S.182, D:K.216, C:D.8, C:D.9, C:D.9 Water bridges: D:D.157

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: S.269, H.270, K.275, E.304, D.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.269, A:H.270 Water bridges: A:A.325 EDO.5: 3 residues within 4Å: Chain A: S.31, L.133, N.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.137 EDO.12: 3 residues within 4Å: Chain C: S.134, N.137, M.138 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.134

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 6 residues within 4Å: Chain C: R.40, R.82, E.86, L.89, L.90, I.91 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.40, C:R.40, C:R.82, C:E.86, C:L.89, C:I.91 Water bridges: C:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heyes, L.C. et al., Structure of Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu98Ala variant at 2.42 Angstroms resolution. To Be Published

Release Date

2016-08-10

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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