SMTL ID : 6gtb.1

17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with FB211

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: FBK.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.186 Hydrogen bonds: A:G.18, A:G.20, A:R.21, A:I.23, A:K.43, A:K.43, A:D.44, A:D.64, A:D.64, A:V.65, A:N.91, A:K.160, A:I.189, A:I.189, A:T.191, A:L.193 Water bridges: A:G.24, A:N.91 Salt bridges: A:R.21 NAD.7: 31 residues within 4Å: Chain B: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: FBK.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.186 Hydrogen bonds: B:G.18, B:G.20, B:R.21, B:I.23, B:K.43, B:K.43, B:D.44, B:D.64, B:D.64, B:V.65, B:N.91, B:K.160, B:I.189, B:I.189, B:T.191, B:L.193 Water bridges: B:G.24, B:N.91 Salt bridges: B:R.21 NAD.13: 31 residues within 4Å: Chain C: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: FBK.16 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.186 Hydrogen bonds: C:G.18, C:G.20, C:R.21, C:I.23, C:K.43, C:K.43, C:D.44, C:D.64, C:V.65, C:N.91, C:K.160, C:I.189, C:I.189, C:T.191, C:L.193 Water bridges: C:G.24, C:N.91 Salt bridges: C:R.21 NAD.19: 31 residues within 4Å: Chain D: G.18, G.20, R.21, G.22, I.23, G.24, D.42, K.43, D.44, C.63, D.64, V.65, T.66, N.91, A.92, G.93, L.115, I.141, S.142, S.143, Y.156, K.160, P.186, G.187, N.188, I.189, T.191, P.192, L.193, W.194 Ligands: FBK.22 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:P.186 Hydrogen bonds: D:G.18, D:G.20, D:R.21, D:I.23, D:K.43, D:K.43, D:D.44, D:D.64, D:V.65, D:N.91, D:K.160, D:I.189, D:I.189, D:T.191, D:L.193 Water bridges: D:G.24, D:N.91 Salt bridges: D:R.21

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

NA.2: 5 residues within 4Å: Chain A: E.52, L.55, P.56, G.57, A.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.52, A:G.57, A:A.58 NA.8: 5 residues within 4Å: Chain B: E.52, L.55, P.56, G.57, A.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.52, B:G.57, B:A.58 NA.14: 5 residues within 4Å: Chain C: E.52, L.55, P.56, G.57, A.58 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.52, C:G.57, C:A.58 NA.20: 5 residues within 4Å: Chain D: E.52, L.55, P.56, G.57, A.58 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.55, D:G.57, D:A.58

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

BGC.3: 6 residues within 4Å: Chain A: G.22, W.190, T.191, P.192, E.195, P.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.22, A:G.22, A:W.190, A:E.195 BGC.9: 6 residues within 4Å: Chain B: G.22, W.190, T.191, P.192, E.195, P.223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.22, B:G.22, B:W.190, B:E.195 BGC.15: 6 residues within 4Å: Chain C: G.22, W.190, T.191, P.192, E.195, P.223 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.22, C:G.22, C:W.190, C:E.195, C:E.195 BGC.21: 6 residues within 4Å: Chain D: G.22, W.190, T.191, P.192, E.195, P.223 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.22, D:G.22, D:W.190, D:E.195, D:E.195

4 x FBK: 3-[6-(3-hydroxyphenyl)pyridin-2-yl]benzoic acid(Non-covalent)

FBK.4: 17 residues within 4Å: Chain A: H.95, P.98, S.143, V.145, Q.150, A.151, Q.152, A.153, Y.156, L.193, W.194, L.197, M.201, T.207 Chain D: Y.255 Ligands: NAD.1, DMS.6 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:H.95, A:P.98, A:L.193, A:W.194, A:L.197, A:L.197 Hydrogen bonds: A:H.95, A:S.143, A:Q.150, A:A.151, A:Y.156, D:Y.255 Water bridges: A:Q.99 pi-Cation interactions: A:H.95 FBK.10: 17 residues within 4Å: Chain B: H.95, P.98, S.143, V.145, Q.150, A.151, Q.152, A.153, Y.156, L.193, W.194, L.197, M.201, T.207 Chain C: Y.255 Ligands: NAD.7, DMS.12 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:H.95, B:P.98, B:L.193, B:W.194, B:L.197, B:L.197 Hydrogen bonds: B:H.95, B:S.143, B:Q.150, B:A.151, B:Y.156, C:Y.255 Water bridges: B:Q.99 pi-Cation interactions: B:H.95 FBK.16: 17 residues within 4Å: Chain B: Y.255 Chain C: H.95, P.98, S.143, V.145, Q.150, A.151, Q.152, A.153, Y.156, L.193, W.194, L.197, M.201, T.207 Ligands: NAD.13, DMS.18 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:H.95, C:P.98, C:L.193, C:W.194, C:L.197, C:L.197 Hydrogen bonds: C:H.95, C:S.143, C:Q.150, C:A.151, C:Y.156, B:Y.255 Water bridges: C:Q.99 pi-Cation interactions: C:H.95 FBK.22: 17 residues within 4Å: Chain A: Y.255 Chain D: H.95, P.98, S.143, V.145, Q.150, A.151, Q.152, A.153, Y.156, L.193, W.194, L.197, M.201, T.207 Ligands: NAD.19, DMS.24 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:H.95, D:P.98, D:L.193, D:W.194, D:L.197, D:L.197 Hydrogen bonds: D:H.95, D:S.143, D:Q.150, D:A.151, D:Y.156, A:Y.255 Water bridges: D:Q.99 pi-Cation interactions: D:H.95

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 2 residues within 4Å: Chain A: Q.107, R.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.110 Water bridges: A:R.110 EDO.11: 2 residues within 4Å: Chain B: Q.107, R.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.110 Water bridges: B:R.110 EDO.17: 2 residues within 4Å: Chain C: Q.107, R.110 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.110 Water bridges: C:R.110 EDO.23: 2 residues within 4Å: Chain D: Q.107, R.110 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.110 Water bridges: D:R.110

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

DMS.6: 7 residues within 4Å: Chain A: Q.150, N.188, W.194, T.207, G.211 Chain D: Y.255 Ligands: FBK.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.150 DMS.12: 7 residues within 4Å: Chain B: Q.150, N.188, W.194, T.207, G.211 Chain C: Y.255 Ligands: FBK.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.150 DMS.18: 7 residues within 4Å: Chain B: Y.255 Chain C: Q.150, N.188, W.194, T.207, G.211 Ligands: FBK.16 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Q.150 DMS.24: 7 residues within 4Å: Chain A: Y.255 Chain D: Q.150, N.188, W.194, T.207, G.211 Ligands: FBK.22 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertoletti, N. et al., X-ray Crystallographic Fragment screening and Hit Optimization. To Be Published

Release Date

2019-09-11

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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