SMTL ID : 6bfg.1

Crystal structure of monotopic membrane protein (S)-mandelate dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 26 residues within 4Å: Chain A: Y.26, L.27, G.78, P.79, T.80, G.81, S.108, A.110, Q.129, Y.131, T.156, K.250, S.272, H.274, G.275, R.277, D.303, S.304, G.305, F.306, R.307, L.325, G.326, R.327, L.330 Ligands: GOL.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.26, A:T.80, A:R.327 Hydrogen bonds: A:G.81, A:S.108, A:Q.129, A:Y.131, A:T.156, A:K.250, A:S.272, A:S.272, A:S.304, A:G.305, A:G.326, A:R.327 Water bridges: A:H.274, A:D.303, A:D.303, A:F.306, A:F.306, A:R.327, A:R.327 Salt bridges: A:R.307, A:R.327 FMN.12: 25 residues within 4Å: Chain B: Y.26, L.27, G.78, P.79, T.80, G.81, S.108, A.110, Q.129, Y.131, T.156, K.250, S.272, H.274, G.275, R.277, D.303, S.304, G.305, F.306, R.307, G.326, R.327, L.330 Ligands: GOL.14 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.26, B:T.80, B:R.327 Hydrogen bonds: B:G.81, B:S.108, B:Q.129, B:Y.131, B:T.156, B:K.250, B:S.272, B:S.272, B:S.304, B:G.305, B:G.326, B:R.327 Water bridges: B:H.274, B:D.303, B:D.303, B:F.306, B:R.327, B:R.327 Salt bridges: B:R.307, B:R.327 FMN.20: 26 residues within 4Å: Chain C: Y.26, L.27, G.78, P.79, T.80, G.81, S.108, A.110, Q.129, Y.131, T.156, K.250, S.272, H.274, G.275, R.277, D.303, S.304, G.305, F.306, R.307, L.325, G.326, R.327, L.330 Ligands: GOL.23 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:Y.26, C:T.80, C:R.327 Hydrogen bonds: C:G.81, C:S.108, C:Q.129, C:Y.131, C:T.156, C:K.250, C:S.272, C:S.272, C:S.304, C:G.305, C:G.326, C:R.327 Water bridges: C:H.274, C:D.303, C:D.303, C:F.306, C:F.306, C:R.327, C:R.327 Salt bridges: C:R.307, C:R.327 FMN.31: 25 residues within 4Å: Chain D: Y.26, L.27, G.78, P.79, T.80, G.81, S.108, A.110, Q.129, Y.131, T.156, K.250, S.272, H.274, G.275, R.277, D.303, S.304, G.305, F.306, R.307, G.326, R.327, L.330 Ligands: GOL.33 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:Y.26, D:T.80, D:R.327 Hydrogen bonds: D:G.81, D:S.108, D:Q.129, D:Y.131, D:T.156, D:K.250, D:S.272, D:S.272, D:S.304, D:G.305, D:G.326, D:R.327 Water bridges: D:H.274, D:D.303, D:D.303, D:F.306, D:R.327, D:R.327 Salt bridges: D:R.307, D:R.327

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: W.87, P.88, D.196 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.192, A:D.196 GOL.3: 4 residues within 4Å: Chain A: R.192, L.195, D.196 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.196, A:D.196 GOL.4: 9 residues within 4Å: Chain A: Y.26, G.81, A.110, Y.131, V.159, R.165, H.274, R.277 Ligands: FMN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.131, A:R.165, A:R.165, A:H.274, A:R.277, A:R.277 GOL.14: 9 residues within 4Å: Chain B: Y.26, G.81, A.110, Y.131, V.159, R.165, H.274, R.277 Ligands: FMN.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.26, B:G.81, B:Y.131, B:Y.131, B:R.165, B:H.274, B:R.277, B:R.277 GOL.21: 4 residues within 4Å: Chain C: W.87, P.88, D.196 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.192, C:D.196 GOL.22: 4 residues within 4Å: Chain C: R.192, L.195, D.196 Ligands: GOL.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.196, C:D.196 GOL.23: 9 residues within 4Å: Chain C: Y.26, G.81, A.110, Y.131, V.159, R.165, H.274, R.277 Ligands: FMN.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.131, C:R.165, C:R.165, C:H.274, C:R.277, C:R.277 GOL.33: 9 residues within 4Å: Chain D: Y.26, G.81, A.110, Y.131, V.159, R.165, H.274, R.277 Ligands: FMN.31 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Y.26, D:G.81, D:Y.131, D:Y.131, D:R.165, D:H.274, D:R.277, D:R.277

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

SO4.5: 4 residues within 4Å: Chain A: K.21, D.186, L.189, H.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.186, A:D.186 SO4.24: 4 residues within 4Å: Chain C: K.21, D.186, L.189, H.190 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.186, C:D.186

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

EDO.6: 4 residues within 4Å: Chain A: C.188, P.191, S.194, V.198 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain A: Y.179, V.184 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: R.12, Y.24, E.28, E.34, V.37, R.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.12, A:Y.24, A:E.34, A:R.167 EDO.9: 11 residues within 4Å: Chain A: K.52, R.53, L.54, V.55, V.57, A.357, Q.358, G.360 Chain D: T.157, D.158, A.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.52, A:R.53, A:L.54, A:V.55 EDO.11: 6 residues within 4Å: Chain A: P.88, K.89, L.92, A.93, R.96, E.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.88 Water bridges: A:R.96 EDO.17: 8 residues within 4Å: Chain A: Y.164 Chain B: F.6, N.7, R.308, L.347, A.350, D.351, R.354 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.354, B:R.354 Water bridges: A:Y.164 EDO.19: 11 residues within 4Å: Chain A: T.157, D.158, A.160 Chain B: K.52, R.53, L.54, V.55, V.57, A.357, Q.358, G.360 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.53, B:L.54, B:V.55, B:V.55, A:A.160 Water bridges: B:Q.358, A:D.158 EDO.25: 4 residues within 4Å: Chain C: C.188, P.191, S.194, V.198 No protein-ligand interaction detected (PLIP) EDO.26: 2 residues within 4Å: Chain C: Y.179, V.184 No protein-ligand interaction detected (PLIP) EDO.27: 6 residues within 4Å: Chain C: R.12, Y.24, E.28, E.34, V.37, R.167 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.12, C:Y.24, C:E.34, C:R.167 EDO.28: 11 residues within 4Å: Chain B: T.157, D.158, A.160 Chain C: K.52, R.53, L.54, V.55, V.57, A.357, Q.358, G.360 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.52, C:R.53, C:L.54, C:V.55 EDO.30: 6 residues within 4Å: Chain C: P.88, K.89, L.92, A.93, R.96, E.338 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.88 Water bridges: C:R.96 EDO.36: 8 residues within 4Å: Chain C: Y.164 Chain D: F.6, N.7, R.308, L.347, A.350, D.351, R.354 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.354, D:R.354 Water bridges: C:Y.164 EDO.38: 11 residues within 4Å: Chain C: T.157, D.158, A.160 Chain D: K.52, R.53, L.54, V.55, V.57, A.357, Q.358, G.360 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.53, D:L.54, D:V.55, D:V.55, C:A.160 Water bridges: D:Q.358, C:D.158

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.10: 5 residues within 4Å: Chain A: K.17, L.189, H.190, P.191, R.192 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.192 CIT.29: 5 residues within 4Å: Chain C: K.17, L.189, H.190, P.191, R.192 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.192

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

PEG.13: 3 residues within 4Å: Chain B: R.192, L.195, D.196 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.192, B:D.196, B:D.196 PEG.32: 3 residues within 4Å: Chain D: R.192, L.195, D.196 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.192, D:D.196, D:D.196

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 4 residues within 4Å: Chain B: K.21, D.186, L.189, H.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.186 PO4.34: 4 residues within 4Å: Chain D: K.21, D.186, L.189, H.190 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.186

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

NA.16: 4 residues within 4Å: Chain B: S.114, I.115, E.116, K.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.116 Water bridges: B:S.114, B:S.114 NA.35: 4 residues within 4Å: Chain D: S.114, I.115, E.116, K.144 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.116, D:E.116 Water bridges: D:S.114

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.18: 20 residues within 4Å: Chain B: P.20, M.22, V.23, Y.26, L.82, A.85, N.162, F.173, K.174, I.175, M.177, S.178, V.183, D.186, G.187, W.193, F.197, M.202, P.203, L.216 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.173, B:F.173 LMT.37: 20 residues within 4Å: Chain D: P.20, M.22, V.23, Y.26, L.82, A.85, N.162, F.173, K.174, I.175, M.177, S.178, V.183, D.186, G.187, W.193, F.197, M.202, P.203, L.216 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.173, D:F.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sukumar, N. et al., Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2 angstrom resolution. Biochimie (2018)

Release Date

2018-08-15

Peptides

(S)-mandelate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

(S)-mandelate dehydrogenase