SMTL ID : 6h0m.1

17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 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.5: 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.9: 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.13: 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 NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 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, H.93, L.113, I.139, S.140, S.141, Y.154, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: DMS.3 23 PLIP interactions: 23 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:D.42, A:D.62, A:D.62, A:V.63, A:N.89, A:Y.154, A:I.187, A:I.187, 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.6: 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, H.93, L.113, I.139, S.140, S.141, Y.154, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: DMS.7 23 PLIP interactions: 23 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:D.42, B:D.62, B:D.62, B:V.63, B:N.89, B:Y.154, B:I.187, B:I.187, 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.10: 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, H.93, L.113, I.139, S.140, S.141, Y.154, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: DMS.11 22 PLIP interactions: 22 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:D.42, C:D.62, C:V.63, C:N.89, C:Y.154, C:I.187, C:I.187, 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.14: 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, H.93, L.113, I.139, S.140, S.141, Y.154, P.184, G.185, N.186, I.187, T.189, P.190, L.191, W.192 Ligands: DMS.15 22 PLIP interactions: 22 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:D.42, D:D.62, D:V.63, D:N.89, D:Y.154, D:I.187, D:I.187, 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 DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 10 residues within 4Å: Chain A: A.90, G.91, N.114, I.139, S.140, Y.154, T.157, A.158, V.161 Ligands: NAD.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.154 DMS.7: 10 residues within 4Å: Chain B: A.90, G.91, N.114, I.139, S.140, Y.154, T.157, A.158, V.161 Ligands: NAD.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.154 DMS.11: 10 residues within 4Å: Chain C: A.90, G.91, N.114, I.139, S.140, Y.154, T.157, A.158, V.161 Ligands: NAD.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.154 DMS.15: 10 residues within 4Å: Chain D: A.90, G.91, N.114, I.139, S.140, Y.154, T.157, A.158, V.161 Ligands: NAD.14 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.154

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

BGC.4: 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.8: 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.12: 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.16: 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

Links

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Citation

Badran, M. et al., 17beta-hydroxysteroid dehydrogenase type 14 mutant K158A in complex with Nicotinamide Adenine Dinucleotide. To Be Published

Release Date

2019-07-31

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