SMTL ID : 3hww.1

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 10 residues within 4Å: Chain A: S.391, L.392, R.395, G.441, D.442, L.443, S.444, G.471 Ligands: MG.2, NA.20 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.391, A:L.392, A:L.443, A:S.444 Water bridges: A:D.442, A:D.442 Salt bridges: A:R.395 AKG.25: 11 residues within 4Å: Chain B: E.369, S.391, L.392, V.393, G.441, D.442, L.443, S.444, V.467, N.469 Ligands: MG.26 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.392 Hydrogen bonds: B:L.392, B:V.393, B:L.443, B:N.469

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.442, V.467, N.469, G.471 Ligands: AKG.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.442, H2O.7 MG.26: 4 residues within 4Å: Chain B: D.442, V.467, N.469 Ligands: AKG.25 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.442

37 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: H.21, D.153, G.157, L.200, R.201, E.202 Ligand excluded by PLIP NA.4: 3 residues within 4Å: Chain A: T.19, G.22, V.23 Ligand excluded by PLIP NA.5: 7 residues within 4Å: Chain A: D.54, R.56, Y.447, D.448, N.450 Chain B: R.56 Ligands: NA.6 Ligand excluded by PLIP NA.6: 6 residues within 4Å: Chain A: Y.447, D.448, L.449, N.450 Chain B: N.450 Ligands: NA.5 Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain A: S.79, G.80, T.81, A.82 Ligand excluded by PLIP NA.9: 5 residues within 4Å: Chain A: P.123, S.135, L.136, N.167, P.169 Ligand excluded by PLIP NA.10: 2 residues within 4Å: Chain A: H.132, S.133 Ligand excluded by PLIP NA.11: 2 residues within 4Å: Chain A: D.179, D.180 Ligand excluded by PLIP NA.12: 5 residues within 4Å: Chain A: P.144, A.145, R.146, R.188 Ligands: GOL.23 Ligand excluded by PLIP NA.13: 3 residues within 4Å: Chain A: Q.211, R.212, D.213 Ligand excluded by PLIP NA.14: 3 residues within 4Å: Chain A: S.208, E.209 Ligands: NA.15 Ligand excluded by PLIP NA.15: 4 residues within 4Å: Chain A: S.208, R.325, L.326 Ligands: NA.14 Ligand excluded by PLIP NA.16: 5 residues within 4Å: Chain A: V.252, Q.255, L.403, V.409 Ligands: NA.17 Ligand excluded by PLIP NA.17: 6 residues within 4Å: Chain A: Q.255, L.403, P.404, Y.407, V.409 Ligands: NA.16 Ligand excluded by PLIP NA.18: 5 residues within 4Å: Chain A: D.264, G.291, R.395, D.398, A.399 Ligand excluded by PLIP NA.19: 4 residues within 4Å: Chain A: R.315, L.316, D.317, R.325 Ligand excluded by PLIP NA.20: 7 residues within 4Å: Chain A: N.390, S.391, L.421, V.440, G.441, S.444 Ligands: AKG.1 Ligand excluded by PLIP NA.22: 3 residues within 4Å: Chain A: A.270, K.271, S.274 Ligand excluded by PLIP NA.27: 6 residues within 4Å: Chain B: W.10, L.136, P.137, P.139, C.168, P.169 Ligand excluded by PLIP NA.28: 7 residues within 4Å: Chain B: A.17, R.20, V.149, D.153, W.192, P.198, W.199 Ligand excluded by PLIP NA.29: 5 residues within 4Å: Chain B: A.66, K.70, Q.71, E.98, K.99 Ligand excluded by PLIP NA.30: 5 residues within 4Å: Chain B: A.29, P.30, E.55, V.77, T.78 Ligand excluded by PLIP NA.31: 6 residues within 4Å: Chain B: T.96, R.228, S.411, N.412, R.413 Ligands: NA.32 Ligand excluded by PLIP NA.32: 5 residues within 4Å: Chain B: K.67, Y.410, S.411 Ligands: NA.31, NA.41 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain B: G.124, M.125, F.126, A.127, H.165 Ligand excluded by PLIP NA.34: 3 residues within 4Å: Chain B: P.137, R.138 Ligands: CL.36 Ligand excluded by PLIP NA.35: 2 residues within 4Å: Chain B: T.140 Ligands: CL.36 Ligand excluded by PLIP NA.38: 3 residues within 4Å: Chain B: S.150, W.199, L.200 Ligand excluded by PLIP NA.40: 2 residues within 4Å: Chain B: I.308, R.324 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain B: T.96, E.98, R.228 Ligands: NA.32 Ligand excluded by PLIP NA.42: 1 residues within 4Å: Chain B: D.142 Ligand excluded by PLIP NA.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.44: 7 residues within 4Å: Chain B: L.248, I.249, G.250, Q.258, P.259, L.260 Ligands: NA.45 Ligand excluded by PLIP NA.45: 4 residues within 4Å: Chain B: G.250, L.260, A.263 Ligands: NA.44 Ligand excluded by PLIP NA.46: 4 residues within 4Å: Chain B: D.264, G.291, K.292, R.395 Ligand excluded by PLIP NA.47: 3 residues within 4Å: Chain B: K.292, L.295, Q.296 Ligand excluded by PLIP NA.48: 7 residues within 4Å: Chain B: G.389, N.390, S.391, L.421, V.440, G.441, S.444 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: A.66, K.70, Q.71, E.98, K.99 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain B: R.138 Ligands: NA.34, NA.35 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 7 residues within 4Å: Chain A: S.416, G.417, I.418 Chain B: E.55, T.81, A.82, Q.118 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.416, A:I.418, B:E.55, B:E.55, B:A.82 GOL.23: 8 residues within 4Å: Chain A: Q.141, D.142, I.143, P.144, A.145, W.185, R.188 Ligands: NA.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.142, A:A.145, A:W.185, A:R.188 GOL.24: 2 residues within 4Å: Chain A: K.507, Y.508 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.508 Water bridges: A:R.510 GOL.37: 3 residues within 4Å: Chain B: H.132, S.133, H.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.133, B:S.133, B:H.154 GOL.39: 3 residues within 4Å: Chain B: Q.186, Q.187, W.193 No protein-ligand interaction detected (PLIP) GOL.49: 3 residues within 4Å: Chain B: N.494, H.496, R.510 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.494, B:R.510, B:R.510

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Priyadarshi, A. et al., Structural and functional analysis of Vitamin K2 synthesis protein MenD. Biochem.Biophys.Res.Commun. (2009)

Release Date

2009-11-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

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

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