SMTL ID : 4ucg.1

NmeDAH7PS R126S variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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: 6 residues within 4Å: Chain B: C.63, K.99, H.270, E.304, D.324 Ligands: PEP.7 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.11 MN.11: 5 residues within 4Å: Chain C: C.63, H.270, E.304, D.324 Ligands: PEP.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.63, C:H.270, C:E.304, C:D.324 MN.13: 5 residues within 4Å: Chain D: C.63, H.270, E.304, D.324 Ligands: PEP.14 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.25

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 12 residues within 4Å: Chain A: R.94, Y.96, K.99, E.145, G.165, A.166, R.167, K.188, R.236, H.270, E.304 Ligands: MN.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.166 Water bridges: A:R.94, A:K.99, A:E.145, A:R.167, A:R.167, A:R.167 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.7: 14 residues within 4Å: Chain B: 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 Ligands: MN.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.100 Hydrogen bonds: B:A.166 Water bridges: B:R.94, B:R.167, B:R.167, B:K.188 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.12: 12 residues within 4Å: Chain C: R.94, Y.96, K.99, E.145, G.165, A.166, R.167, K.188, R.236, H.270, E.304 Ligands: MN.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.166 Water bridges: C:Y.96, C:R.167, C:R.167 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 PEP.14: 13 residues within 4Å: Chain D: 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.13 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:A.166 Water bridges: D:R.94, 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

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

SO4.3: 2 residues within 4Å: Chain A: R.101, T.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.102, A:T.102 Water bridges: A:T.103 Salt bridges: A:R.101 SO4.8: 2 residues within 4Å: Chain B: R.101, T.102 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.102, B:T.102 Water bridges: B:R.101, B:D.324 Salt bridges: B:R.101 SO4.15: 2 residues within 4Å: Chain D: R.101, T.102 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.102, D:T.102, D:T.102 Salt bridges: D:R.101

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

PEG.4: 7 residues within 4Å: Chain A: L.19, A.23, E.27 Chain C: L.19, A.23, E.27 Ligands: PEG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.27 PEG.5: 5 residues within 4Å: Chain A: Y.26, E.27 Chain C: L.19, N.122 Ligands: PEG.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.27, C:N.122 PEG.9: 6 residues within 4Å: Chain B: W.106, D.112, L.115, D.116, G.117, I.322 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.117 PEG.10: 5 residues within 4Å: Chain A: A.221, I.222 Chain B: K.16, E.17, L.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.18, A:I.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cross, P.J. et al., The Functional Unit of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase is Dimeric. Plos One (2016)

Release Date

2016-01-13

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