SMTL ID : 6zr6.1

17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with non-steroidal inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

BGC.1: 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:E.193, A:E.193 Water bridges: A:G.20 BGC.5: 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:E.193, B:E.193 Water bridges: B:G.20 BGC.9: 6 residues within 4Å: Chain C: G.20, W.188, T.189, P.190, E.193, P.221 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.20, C:E.193 Water bridges: C:G.20 BGC.13: 6 residues within 4Å: Chain D: G.20, W.188, T.189, P.190, E.193, P.221 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.20, D:E.193 Water bridges: D:G.20

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

NAD.2: 27 residues within 4Å: Chain A: G.16, R.19, G.20, I.21, D.40, K.41, C.61, D.62, V.63, 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 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.21, A:P.184 Hydrogen bonds: A:G.16, A:G.18, A:R.19, A:I.21, A:K.41, A:K.41, A:D.62, A:D.62, A:V.63, A:N.89, A:Y.154, A:K.158, A:I.187, A:I.187, A:T.189, A:T.189, A:L.191 Water bridges: A:G.22, A:D.40, A:D.40, A:N.89 Salt bridges: A:R.19 NAD.6: 27 residues within 4Å: Chain B: G.16, R.19, G.20, I.21, D.40, K.41, C.61, D.62, V.63, 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: F45.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.21, B:P.184 Hydrogen bonds: B:G.16, B:G.18, B:R.19, B:I.21, B:K.41, B:K.41, B:D.62, B:D.62, B:V.63, B:N.89, B:Y.154, B:K.158, B:I.187, B:I.187, B:T.189, B:T.189, B:L.191 Water bridges: B:G.22, B:D.40, B:D.40, B:N.89 Salt bridges: B:R.19 NAD.10: 27 residues within 4Å: Chain C: G.16, R.19, G.20, I.21, D.40, K.41, C.61, D.62, V.63, 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: F45.12 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.21, C:P.184 Hydrogen bonds: C:G.16, C:G.18, C:R.19, C:I.21, C:K.41, 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 Water bridges: C:G.22, C:D.40, C:D.40, C:T.64, C:N.89 Salt bridges: C:R.19 NAD.14: 27 residues within 4Å: Chain D: G.16, R.19, G.20, I.21, D.40, K.41, C.61, D.62, V.63, 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 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.21, D:P.184 Hydrogen bonds: D:G.16, D:G.18, D:R.19, D:I.21, D:K.41, 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 Water bridges: D:G.22, D:D.40, D:D.40, D:T.64, D:N.89 Salt bridges: D:R.19

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

NA.3: 4 residues within 4Å: Chain A: E.50, L.53, P.54, A.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.55, A:A.56, A:A.56 NA.7: 4 residues within 4Å: Chain B: E.50, L.53, P.54, A.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.53, B:G.55, B:A.56 NA.11: 4 residues within 4Å: Chain C: E.50, L.53, P.54, A.56 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.50, C:G.55, C:A.56 NA.15: 4 residues within 4Å: Chain D: E.50, L.53, P.54, A.56 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.55, D:A.56, D:A.56

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

F45.4: 17 residues within 4Å: Chain A: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195 Chain C: Y.253 Ligands: NAD.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.154, A:W.192, A:W.192, A:W.192, A:L.195, A:L.195, C:Y.253 Hydrogen bonds: A:H.93, A:S.141, A:S.141, A:Q.148 pi-Stacking: A:H.93 F45.8: 17 residues within 4Å: Chain B: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195 Chain D: Y.253 Ligands: NAD.6 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain B Hydrophobic interactions: D:Y.253, B:Y.154, B:W.192, 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 pi-Stacking: B:H.93 F45.12: 17 residues within 4Å: Chain A: Y.253 Chain C: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195 Ligands: NAD.10 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.154, C:W.192, C:W.192, C:W.192, C:L.195, C:L.195, A:Y.253 Hydrogen bonds: C:H.93, C:S.141, C:S.141, C:Q.148, C:Y.154 pi-Stacking: C:H.93 F45.16: 17 residues within 4Å: Chain B: Y.253 Chain D: H.93, P.96, S.141, V.143, Q.148, A.149, Q.150, A.151, Y.154, P.184, G.185, N.186, L.191, W.192, L.195 Ligands: NAD.14 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.154, D:W.192, D:W.192, D:W.192, D:L.195, D:L.195, B:Y.253 Hydrogen bonds: D:H.93, D:S.141, D:S.141, D:Q.148, D:Y.154 pi-Stacking: D:H.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Badran, M.J. et al., 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with non-steroidal inhibitor. To Be Published

Release Date

2021-07-21

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

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