SMTL ID : 5d02.1

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Glu176Gln variant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 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.4: 5 residues within 4Å: Chain B: C.63, H.270, E.304, D.324 Ligands: PEP.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.63, B:H.270, B:E.304, B:D.324, H2O.12 MN.8: 6 residues within 4Å: Chain C: C.63, R.94, H.270, E.304, D.324 Ligands: PEP.9 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.14 MN.12: 5 residues within 4Å: Chain D: C.63, H.270, E.304, D.324 Ligands: PEP.13 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.20

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 13 residues within 4Å: Chain A: R.94, Y.96, K.99, P.100, E.145, G.165, A.166, R.167, K.188, R.236, H.270, E.304 Ligands: MN.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.100 Hydrogen bonds: A:A.166 Water bridges: A:K.99, A:K.99, A:K.99, A:E.145, A:R.167, A:R.236 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 PEP.5: 13 residues within 4Å: Chain B: R.94, Y.96, K.99, E.145, G.165, A.166, R.167, K.188, R.236, H.270, M.302, E.304 Ligands: MN.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Y.96, B:A.166 Water bridges: B:K.99, B:E.145, 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 PEP.9: 11 residues within 4Å: Chain C: R.94, Y.96, E.145, G.165, A.166, R.167, K.188, R.236, H.270, M.302 Ligands: MN.8 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:A.166 Water bridges: C:R.94, C:Y.96, C:R.167 Salt bridges: C:R.94, C:R.167, C:K.188, C:K.188, C:R.236, C:H.270, C:H.270 PEP.13: 13 residues within 4Å: Chain D: R.94, Y.96, K.99, P.100, E.145, G.165, A.166, R.167, K.188, R.236, H.270, E.304 Ligands: MN.12 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.100 Hydrogen bonds: D:A.166 Water bridges: D:K.99, D:K.99, D:K.99, D:E.145, D:R.167, D:R.167, D:R.167 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

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

SO4.3: 2 residues within 4Å: Chain A: R.101, T.102 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.102, A:T.102, A:T.102 Water bridges: A:R.101, A:T.103, A:T.103 Salt bridges: A:R.101 SO4.15: 3 residues within 4Å: Chain D: R.101, T.102 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.102, D:T.102 Salt bridges: D:R.101

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

EDO.6: 5 residues within 4Å: Chain A: I.222 Chain B: F.119, D.120, I.121, N.122 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Water bridges: D:Y.26 Hydrogen bonds: B:D.120, B:D.120, B:N.122, B:N.122 EDO.7: 2 residues within 4Å: Chain B: L.115, G.117 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain C: H.224, T.225, G.226 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.224 EDO.11: 3 residues within 4Å: Chain C: S.31, L.133, N.137 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.137 EDO.14: 5 residues within 4Å: Chain D: R.101, R.311, T.323, D.324 Ligands: SO4.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.101, D:R.311, D:D.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heyes, L.C., Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Glu176Gln variant at 1.87 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