SMTL ID : 6emm.1

17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with Salicylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 29 residues within 4Å: Chain A: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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: SAL.3 18 PLIP interactions: 18 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:D.64, A:D.64, A:V.65, A:N.91, A:Y.156, A:K.160, A:I.189, A:I.189, A:L.193 Water bridges: A:G.24, A:N.91 Salt bridges: A:R.21 NAD.5: 29 residues within 4Å: Chain B: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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: SAL.7 18 PLIP interactions: 18 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:D.64, B:D.64, B:V.65, B:N.91, B:Y.156, B:K.160, B:I.189, B:I.189, B:L.193 Water bridges: B:G.24, B:N.91 Salt bridges: B:R.21 NAD.9: 29 residues within 4Å: Chain C: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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: SAL.11 17 PLIP interactions: 17 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: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.13: 29 residues within 4Å: Chain D: G.18, G.20, R.21, G.22, I.23, D.42, K.43, D.44, C.63, D.64, V.65, 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: SAL.15 17 PLIP interactions: 17 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: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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: W.190, E.195, R.205, I.208 Chain D: P.268, D.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.195, A:R.205 PEG.6: 6 residues within 4Å: Chain B: W.190, E.195, R.205, I.208 Chain C: P.268, D.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.195, B:R.205 PEG.10: 6 residues within 4Å: Chain B: P.268, D.269 Chain C: W.190, E.195, R.205, I.208 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.205 PEG.14: 6 residues within 4Å: Chain A: P.268, D.269 Chain D: W.190, E.195, R.205, I.208 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.205

4 x SAL: 2-HYDROXYBENZOIC ACID(Non-covalent)

SAL.3: 11 residues within 4Å: Chain A: H.95, S.143, V.145, Q.150, Y.156, N.188, L.193, W.194, L.197 Chain D: Y.255 Ligands: NAD.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:H.95, A:L.193, A:L.197 Hydrogen bonds: A:S.143, A:Q.150, D:Y.255 pi-Cation interactions: A:H.95 SAL.7: 11 residues within 4Å: Chain B: H.95, S.143, V.145, Q.150, Y.156, N.188, L.193, W.194, L.197 Chain C: Y.255 Ligands: NAD.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:H.95, B:L.193, B:L.197 Hydrogen bonds: B:S.143, B:Q.150, C:Y.255 pi-Cation interactions: B:H.95 SAL.11: 11 residues within 4Å: Chain B: Y.255 Chain C: H.95, S.143, V.145, Q.150, Y.156, N.188, L.193, W.194, L.197 Ligands: NAD.9 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:H.95, C:L.193, C:L.197 Hydrogen bonds: C:S.143, C:Q.150, C:Y.156 pi-Cation interactions: C:H.95 SAL.15: 11 residues within 4Å: Chain A: Y.255 Chain D: H.95, S.143, V.145, Q.150, Y.156, N.188, L.193, W.194, L.197 Ligands: NAD.13 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:H.95, D:L.193, D:L.197 Hydrogen bonds: D:S.143, D:Q.150, D:Y.156 pi-Cation interactions: D:H.95

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 7 residues within 4Å: Chain A: A.147, E.244, L.246 Chain C: A.147, E.244, L.246 Ligands: PG4.12 No protein-ligand interaction detected (PLIP) PG4.8: 7 residues within 4Å: Chain B: A.147, E.244, L.246 Chain D: A.147, E.244, L.246 Ligands: PG4.16 No protein-ligand interaction detected (PLIP) PG4.12: 7 residues within 4Å: Chain A: A.147, E.244, L.246 Chain C: A.147, E.244, L.246 Ligands: PG4.4 No protein-ligand interaction detected (PLIP) PG4.16: 7 residues within 4Å: Chain B: A.147, E.244, L.246 Chain D: A.147, E.244, L.246 Ligands: PG4.8 No protein-ligand interaction detected (PLIP)

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

2018-10-31

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

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