SMTL ID : 6zdi.1

17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 2-fluoro-5-nitrophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 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, 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: QFT.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.21, A:P.184 Hydrogen bonds: A:G.16, A:G.16, A:R.19, A:I.21, A:K.41, A:D.62, A:V.63, A:N.89, A:Y.154, A:K.158, A:G.185, A:I.187, A:T.189, A:L.191 Water bridges: A:G.22, A:N.89 Salt bridges: A:R.19 pi-Cation interactions: A:K.41 NAD.4: 28 residues within 4Å: Chain B: G.16, R.19, G.20, I.21, D.40, K.41, 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: QFT.6 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.21, B:P.184 Hydrogen bonds: B:G.16, B:G.16, B:R.19, B:I.21, B:K.41, B:D.62, B:V.63, B:N.89, B:Y.154, B:K.158, B:G.185, B:I.187, B:T.189, B:L.191 Water bridges: B:G.22, B:N.89 Salt bridges: B:R.19 pi-Cation interactions: B:K.41 NAD.7: 28 residues within 4Å: Chain C: G.16, R.19, G.20, I.21, D.40, K.41, 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: QFT.9 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.21, C:P.184 Hydrogen bonds: C:G.16, 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:G.185, C:I.187, C:T.189, C:L.191 Water bridges: C:G.22, C:N.89 Salt bridges: C:R.19 pi-Cation interactions: C:K.41 NAD.10: 28 residues within 4Å: Chain D: G.16, R.19, G.20, I.21, D.40, K.41, 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: QFT.12 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.21, D:P.184 Hydrogen bonds: D:G.16, 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:G.185, D:I.187, D:T.189, D:L.191 Water bridges: D:G.22, D:N.89 Salt bridges: D:R.19 pi-Cation interactions: D:K.41

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

NA.2: 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.5: 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.8: 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.11: 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 QFT: 2-fluoranyl-5-nitro-phenol(Non-covalent)

QFT.3: 11 residues within 4Å: Chain A: H.93, S.141, V.143, Y.154, P.184, N.186, L.191, W.192, L.195 Chain C: Y.253 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.141, A:Y.154 QFT.6: 11 residues within 4Å: Chain B: H.93, S.141, V.143, Y.154, P.184, N.186, L.191, W.192, L.195 Chain D: Y.253 Ligands: NAD.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.141, B:Y.154 QFT.9: 11 residues within 4Å: Chain A: Y.253 Chain C: H.93, S.141, V.143, Y.154, P.184, N.186, L.191, W.192, L.195 Ligands: NAD.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.141, C:Y.154, C:Y.154 QFT.12: 11 residues within 4Å: Chain B: Y.253 Chain D: H.93, S.141, V.143, Y.154, P.184, N.186, L.191, W.192, L.195 Ligands: NAD.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.141, D:Y.154, D:Y.154

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 2-fluoro-5-nitrophenol. 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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