SMTL ID : 4hso.1

Crystal structure of S213G variant DAH7PS from Neisseria meningitidis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x TYR: TYROSINE(Non-covalent)

TYR.1: 12 residues within 4Å: Chain A: M.149, Q.153, L.177, G.180, L.181, S.182, G.213, V.214, K.216 Chain B: D.8, D.9, I.12 12 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions, 5 interactions with chain B Hydrophobic interactions: A:L.177, B:I.12 Hydrogen bonds: A:M.149, A:Q.153, A:S.182, A:V.214, A:K.216, Y.1, B:D.8, B:D.9, B:D.9, B:D.9 TYR.4: 13 residues within 4Å: Chain A: D.8, D.9, I.12 Chain B: M.149, Q.153, A.156, L.177, G.180, L.181, S.182, G.213, V.214, K.216 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.177, A:I.12 Hydrogen bonds: B:M.149, B:Q.153, B:S.182, B:V.214, B:K.216, A:D.8, A:D.9 TYR.7: 13 residues within 4Å: Chain C: M.149, Q.153, A.156, L.177, G.180, L.181, S.182, G.213, V.214, K.216 Chain D: D.8, D.9, I.12 12 PLIP interactions: 9 interactions with chain C, 1 Ligand-Ligand interactions, 2 interactions with chain D Hydrophobic interactions: C:Q.153, C:L.177 Hydrogen bonds: C:M.149, C:Q.153, C:S.182, C:V.214, C:K.216, D:D.9, D:D.9 Water bridges: C:S.182, C:S.182, Y.7 TYR.10: 12 residues within 4Å: Chain C: D.8, D.9, I.12 Chain D: M.149, Q.153, A.156, L.177, G.180, L.181, S.182, G.213, V.214 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C, Hydrophobic interactions: D:L.177, C:I.12 Hydrogen bonds: D:M.149, D:Q.153, D:S.182, D:V.214, C:D.9

4 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.2: 13 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, M.302, E.304 Ligands: MN.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.166 Water bridges: A:R.94, A:E.145, 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.5: 11 residues within 4Å: Chain B: R.94, Y.96, K.99, E.145, G.165, A.166, K.188, R.236, H.270, E.304 Ligands: MN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.166 Water bridges: B:Y.96 Salt bridges: B:R.94, B:K.99, B:K.188, B:K.188, B:R.236, B:H.270, B:H.270 PEP.8: 10 residues within 4Å: Chain C: R.94, Y.96, K.99, G.165, A.166, K.188, R.236, H.270, E.304 Ligands: MN.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.96, C:A.166 Salt bridges: C:R.94, C:K.99, C:K.188, C:K.188, C:R.236, C:H.270, C:H.270 PEP.11: 12 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, E.304 Ligands: MN.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:A.166 Water bridges: 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

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

MN.3: 5 residues within 4Å: Chain A: C.63, H.270, E.304, D.324 Ligands: PEP.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:H.270, A:E.304, A:D.324 MN.6: 6 residues within 4Å: Chain B: C.63, K.99, H.270, E.304, D.324 Ligands: PEP.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.63, B:H.270, B:E.304, B:D.324 MN.9: 5 residues within 4Å: Chain C: C.63, H.270, E.304, D.324 Ligands: PEP.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.63, C:H.270, C:E.304, C:D.324 MN.12: 6 residues within 4Å: Chain D: C.63, K.99, H.270, E.304, D.324 Ligands: PEP.11 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.63, D:H.270, D:E.304, D:D.324

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cross, P.J. et al., Neisseria meningitidis expresses a single 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase that is inhibited primarily by phenylalanine. Protein Sci. (2013)

Release Date

2013-09-11

Peptides

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase

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