SMTL ID : 5ejm.4 (3 other biounits)

ThDP-Mn2+ complex of R413A variant of EcMenD soaked with 2-ketoglutarate for 35 min

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x TD5: (4~{R})-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid(Non-covalent)

TD5.1: 29 residues within 4Å: Chain A: S.391, L.392, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474, F.475 Chain B: P.30, G.31, S.32, R.33, E.55, T.78, T.81, A.82, N.85, R.107, Q.118 Ligands: MN.2 28 PLIP interactions: 18 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:I.418, A:D.419, A:Y.447, A:F.475, B:P.30, B:T.78 Hydrogen bonds: A:S.391, A:S.391, A:L.392, A:S.416, A:I.418, A:G.441, A:D.442, A:L.443, A:S.444, A:Q.473, A:I.474, B:S.32, B:R.33, B:T.78, B:Q.118 Water bridges: A:V.393, A:N.469, A:N.469, B:S.32, B:T.81, B:A.82 Salt bridges: B:R.107 TD5.5: 29 residues within 4Å: Chain A: P.30, G.31, S.32, R.33, E.55, T.78, T.81, A.82, N.85, R.107, Q.118 Chain B: S.391, L.392, S.416, G.417, I.418, D.419, G.441, D.442, L.443, S.444, Y.447, N.469, G.471, G.472, Q.473, I.474, F.475 Ligands: MN.6 26 PLIP interactions: 9 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:P.30, A:T.78, B:I.418, B:D.419, B:Y.447 Hydrogen bonds: A:S.32, A:R.33, A:T.78, A:Q.118, B:S.391, B:S.391, B:L.392, B:S.416, B:I.418, B:G.441, B:D.442, B:L.443, B:S.444, B:Q.473, B:I.474 Water bridges: A:S.32, A:A.82, B:V.393, B:N.469, B:N.469 Salt bridges: A:R.107

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

MN.2: 4 residues within 4Å: Chain A: D.442, N.469, G.471 Ligands: TD5.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.442, A:G.471, H2O.5 MN.6: 4 residues within 4Å: Chain B: D.442, N.469, G.471 Ligands: TD5.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.442, B:G.471, H2O.26

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: H.49, H.50, T.51, R.430, A.453, L.454, Q.457 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.49, A:T.51, A:T.51, A:R.430, A:R.430, A:L.454 Water bridges: A:Q.457, B:R.487 GOL.7: 7 residues within 4Å: Chain B: H.49, H.50, T.51, R.430, A.453, L.454, Q.457 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.49, B:T.51, B:T.51, B:R.430, B:R.430, B:L.454 Water bridges: B:Q.457, B:Q.457

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

EDO.4: 5 residues within 4Å: Chain A: I.361, R.364, H.374, R.375, D.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.364, A:D.378 Water bridges: A:R.364 EDO.8: 6 residues within 4Å: Chain B: I.361, R.364, H.374, R.375, C.377, D.378 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.364, B:D.378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qin, M.M. et al., Two active site arginines are critical determinants of substrate binding and catalysis in MenD, a thiamine-dependent enzyme in menaquinone biosynthesis. Biochem. J. (2018)

Release Date

2016-11-02

Peptides

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Related Entries With Identical Sequence