SMTL ID : 6gbt.1

17beta-hydroxysteroid dehydrogenase type 14 Mutant Y253A in complex with a non-steroidal inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: G.16, R.19, G.20, I.21, D.40, K.41, D.42, 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: F45.2 25 PLIP interactions: 25 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.42, A:D.42, 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:K.41, A:K.41, A:K.41, A:N.89 Salt bridges: A:R.19 NAD.5: 28 residues within 4Å: Chain B: G.16, R.19, G.20, I.21, D.40, K.41, D.42, 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: F45.6 25 PLIP interactions: 25 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.42, B:D.42, 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:K.41, B:K.41, B:K.41, B:N.89 Salt bridges: B:R.19 NAD.9: 28 residues within 4Å: Chain C: G.16, R.19, G.20, I.21, D.40, K.41, D.42, 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: F45.10 22 PLIP interactions: 22 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.42, 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:K.41, C:K.41, C:K.41, C:N.89 Salt bridges: C:R.19 NAD.13: 28 residues within 4Å: Chain D: G.16, R.19, G.20, I.21, D.40, K.41, D.42, 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: F45.14 22 PLIP interactions: 22 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.42, 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:K.41, D:K.41, D:K.41, D:N.89 Salt bridges: D:R.19

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

F45.2: 15 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, N.186, W.192, L.195 Chain C: Y.253 Ligands: NAD.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.96, A:Y.154, 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 F45.6: 15 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, N.186, W.192, L.195 Chain D: Y.253 Ligands: NAD.5 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:P.96, B:Y.154, B:W.192, B:L.195, B:L.195, D:Y.253 Hydrogen bonds: B:H.93, B:S.141, B:S.141, B:Q.148 pi-Stacking: B:H.93 F45.10: 15 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, N.186, W.192, L.195 Ligands: NAD.9 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:P.96, C:Y.154, 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 F45.14: 15 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, N.186, W.192, L.195 Ligands: NAD.13 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:P.96, D:Y.154, 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

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

DMS.3: 3 residues within 4Å: Chain A: G.81, R.82, K.131 No protein-ligand interaction detected (PLIP) DMS.7: 3 residues within 4Å: Chain B: G.81, R.82, K.131 No protein-ligand interaction detected (PLIP) DMS.11: 3 residues within 4Å: Chain C: G.81, R.82, K.131 No protein-ligand interaction detected (PLIP) DMS.15: 3 residues within 4Å: Chain D: G.81, R.82, K.131 No protein-ligand interaction detected (PLIP)

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

NA.4: 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.8: 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:E.50, B:G.55, B:A.56 NA.12: 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.16: 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

Links

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Citation

Badran, M.J., 17beta Hydroxysteroid Dehydrogenase type 14 mutant C255A in complex with non-steroidal inhibitor. To Be Published

Release Date

2019-04-24

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