SMTL ID : 6g4l.1

17beta-hydroxysteroid Dehydrogenase Type 14 Mutant Y253A in Complex With a Non-steroidal Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 32 residues within 4Å: Chain A: G.16, G.18, R.19, G.20, I.21, G.22, C.39, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: F45.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.21, A:P.184 Hydrogen bonds: A:G.16, A:R.19, A:I.21, A:K.41, A:D.62, A:D.62, A:V.63, A:N.89, A:K.158, A:I.187, A:I.187, A:T.189, A:T.189, A:L.191, A:W.192 Water bridges: A:G.22, A:D.40, A:D.42, A:N.89 Salt bridges: A:R.19 NAD.7: 32 residues within 4Å: Chain B: G.16, G.18, R.19, G.20, I.21, G.22, C.39, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: F45.10 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.21, B:P.184 Hydrogen bonds: B:G.16, B:R.19, B:I.21, B:K.41, B:D.62, B:D.62, B:V.63, B:N.89, B:K.158, B:I.187, B:I.187, B:T.189, B:T.189, B:L.191, B:W.192 Water bridges: B:G.22, B:D.40, B:D.42, B:N.89 Salt bridges: B:R.19 NAD.13: 32 residues within 4Å: Chain C: G.16, G.18, R.19, G.20, I.21, G.22, C.39, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: F45.16 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.21, C:P.184 Hydrogen bonds: C:G.16, C:R.19, C:I.21, C:K.41, C:D.62, C:V.63, C:N.89, C:K.158, C:I.187, C:I.187, C:T.189, C:T.189, C:L.191, C:W.192 Water bridges: C:G.22, C:D.40, C:D.40, C:N.89 Salt bridges: C:R.19 NAD.19: 32 residues within 4Å: Chain D: G.16, G.18, R.19, G.20, I.21, G.22, C.39, D.40, K.41, D.42, C.61, D.62, V.63, T.64, N.89, A.90, G.91, L.113, I.139, S.140, S.141, Y.154, K.158, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: F45.22 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.21, D:P.184 Hydrogen bonds: D:G.16, D:R.19, D:I.21, D:K.41, D:D.62, D:V.63, D:N.89, D:K.158, D:I.187, D:I.187, D:T.189, D:T.189, D:L.191, D:W.192 Water bridges: D:G.22, D:D.40, D:D.40, D:N.89 Salt bridges: D:R.19

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

NA.2: 5 residues within 4Å: Chain A: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.56, A:A.56 NA.8: 5 residues within 4Å: Chain B: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.50, B:A.56 NA.14: 5 residues within 4Å: Chain C: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.53, C:A.56 NA.20: 5 residues within 4Å: Chain D: E.50, L.53, P.54, G.55, A.56 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.56, D:A.56

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.3: 6 residues within 4Å: Chain A: G.20, W.188, T.189, P.190, E.193, P.221 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.20, A:W.188, A:E.193 Water bridges: A:G.20 BGC.9: 6 residues within 4Å: Chain B: G.20, W.188, T.189, P.190, E.193, P.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.20, B:W.188, B:E.193 Water bridges: B:G.20 BGC.15: 6 residues within 4Å: Chain C: G.20, W.188, T.189, P.190, E.193, P.221 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.20, C:W.188, C:E.193, C:E.193 Water bridges: C:G.20 BGC.21: 6 residues within 4Å: Chain D: G.20, W.188, T.189, P.190, E.193, P.221 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.20, D:W.188, D:E.193, D:E.193 Water bridges: D:G.20

4 x F45: [6-(3,4-dihydroxyphenyl)pyridin-2-yl](4-fluoro-3-hydroxyphenyl)methanone(Non-covalent)

F45.4: 19 residues within 4Å: Chain A: H.93, P.96, S.141, L.142, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195, M.199 Ligands: NAD.1, DMS.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.96, A:Y.154, A:W.192, A:W.192, A:L.195, A:L.195 Hydrogen bonds: A:H.93, A:S.141, A:S.141, A:Q.148, A:Q.150, A:Y.154 pi-Stacking: A:H.93 Halogen bonds: A:P.184 F45.10: 19 residues within 4Å: Chain B: H.93, P.96, S.141, L.142, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195, M.199 Ligands: NAD.7, DMS.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.96, B:Y.154, B:W.192, B:W.192, B:L.195, B:L.195 Hydrogen bonds: B:H.93, B:S.141, B:S.141, B:Q.148, B:Q.150, B:Y.154 pi-Stacking: B:H.93 Halogen bonds: B:P.184 F45.16: 19 residues within 4Å: Chain C: H.93, P.96, S.141, L.142, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195, M.199 Ligands: NAD.13, DMS.17 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:P.96, C:Y.154, C:W.192, C:W.192, C:L.195, C:L.195 Hydrogen bonds: C:H.93, C:S.141, C:S.141, C:Q.148, C:Q.150, C:Y.154 pi-Stacking: C:H.93 Halogen bonds: C:P.184 F45.22: 19 residues within 4Å: Chain D: H.93, P.96, S.141, L.142, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195, M.199 Ligands: NAD.19, DMS.23 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:P.96, D:Y.154, D:W.192, D:W.192, D:L.195, D:L.195 Hydrogen bonds: D:H.93, D:S.141, D:S.141, D:Q.148, D:Q.150, D:Y.154 pi-Stacking: D:H.93 Halogen bonds: D:P.184

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 11 residues within 4Å: Chain A: L.142, V.143, I.146, Q.148, G.185, N.186, A.212, Q.213, A.249 Chain C: A.253 Ligands: F45.4 No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: G.81, R.82, K.131, S.132 No protein-ligand interaction detected (PLIP) DMS.11: 11 residues within 4Å: Chain B: L.142, V.143, I.146, Q.148, G.185, N.186, A.212, Q.213, A.249 Chain D: A.253 Ligands: F45.10 No protein-ligand interaction detected (PLIP) DMS.12: 4 residues within 4Å: Chain B: G.81, R.82, K.131, S.132 No protein-ligand interaction detected (PLIP) DMS.17: 11 residues within 4Å: Chain A: A.253 Chain C: L.142, V.143, I.146, Q.148, G.185, N.186, A.212, Q.213, A.249 Ligands: F45.16 No protein-ligand interaction detected (PLIP) DMS.18: 4 residues within 4Å: Chain C: G.81, R.82, K.131, S.132 No protein-ligand interaction detected (PLIP) DMS.23: 11 residues within 4Å: Chain B: A.253 Chain D: L.142, V.143, I.146, Q.148, G.185, N.186, A.212, Q.213, A.249 Ligands: F45.22 No protein-ligand interaction detected (PLIP) DMS.24: 4 residues within 4Å: Chain D: G.81, R.82, K.131, S.132 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Badran, M. et al., Mutational and structural studies uncover crucial amino acids determining activity and stability of 17beta-HSD14. J.Steroid Biochem.Mol.Biol. (2019)

Release Date

2019-04-10

Peptides

17-beta-hydroxysteroid dehydrogenase 14: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

17-beta-hydroxysteroid dehydrogenase 14