SMTL ID : 6zde.1

17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with pentafluorophenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

4 x QFZ: 2,3,4,5,6-pentakis(fluoranyl)phenol(Non-covalent)

QFZ.1: 11 residues within 4Å: Chain A: H.93, S.141, V.143, Q.148, Y.154, N.186, L.191, W.192, L.195 Chain C: Y.253 Ligands: NAD.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.141, A:S.141 pi-Stacking: A:H.93 QFZ.4: 11 residues within 4Å: Chain B: H.93, S.141, V.143, Q.148, Y.154, N.186, L.191, W.192, L.195 Chain D: Y.253 Ligands: NAD.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.141, B:S.141 pi-Stacking: B:H.93 QFZ.7: 11 residues within 4Å: Chain A: Y.253 Chain C: H.93, S.141, V.143, Q.148, Y.154, N.186, L.191, W.192, L.195 Ligands: NAD.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.141, C:S.141, C:Y.154 pi-Stacking: C:H.93 QFZ.10: 11 residues within 4Å: Chain B: Y.253 Chain D: H.93, S.141, V.143, Q.148, Y.154, N.186, L.191, W.192, L.195 Ligands: NAD.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.141, D:S.141, D:Y.154 pi-Stacking: D:H.93

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

NAD.2: 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: QFZ.1 22 PLIP interactions: 22 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.62, A:D.62, A:V.63, A:N.89, A:Y.154, A:K.158, A:I.187, A:I.187, A:L.191 Water bridges: A:R.19, A:G.22, A:D.40, A:D.42, 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: QFZ.4 22 PLIP interactions: 22 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.62, B:D.62, B:V.63, B:N.89, B:Y.154, B:K.158, B:I.187, B:I.187, B:L.191 Water bridges: B:R.19, B:G.22, B:D.40, B:D.42, B:N.89 Salt bridges: B:R.19 NAD.8: 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: QFZ.7 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.62, C:V.63, C:N.89, C:K.158, C:I.187, C:I.187, C:T.189, C:L.191 Water bridges: C:R.19, C:G.22, C:D.40, C:D.40, C:T.64, C:N.89 Salt bridges: C:R.19 NAD.11: 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: QFZ.10 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.62, D:V.63, D:N.89, D:K.158, D:I.187, D:I.187, D:T.189, D:L.191 Water bridges: D:R.19, 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.6: 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.9: 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:L.53, C:G.55, C:A.56 NA.12: 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

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2021-01-13

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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