SMTL ID : 7ry4.1

Multi-conformer model of Ketosteroid Isomerase Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to a transition state analog at 250 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.11 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: G.72, P.73, R.75, P.85 Chain B: T.71, P.85 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: T.71, P.85 Chain B: G.72, P.73, R.75, P.85 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: E.18, D.21, R.67 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.21, H2O.2, H2O.3, H2O.4, H2O.4 MG.4: 1 residues within 4Å: Chain A: R.67 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: E.109, H.110 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: E.18, D.21 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.21, H2O.7, H2O.8, H2O.8, H2O.8 MG.9: 1 residues within 4Å: Chain B: D.21 No protein-ligand interaction detected (PLIP)

2 x J3Z: (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one(Non-covalent)

J3Z.5: 16 residues within 4Å: Chain A: Y.16, V.20, N.40, F.56, F.57, G.60, L.61, V.66, F.86, V.88, M.90, L.99, V.101, D.103, A.118, W.120 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.20, A:V.20, A:F.57, A:L.61, A:V.101 Hydrogen bonds: A:Y.16, A:D.103 Water bridges: A:N.40 pi-Stacking: A:F.86 J3Z.10: 17 residues within 4Å: Chain B: Y.16, V.20, N.40, F.56, F.57, G.60, L.61, V.66, F.86, V.88, M.90, L.99, V.101, D.103, M.116, A.118, W.120 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.57, B:F.86, B:V.88, B:L.99, B:A.118 Hydrogen bonds: B:Y.16, B:Y.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yabukarski, F. et al., Ensemble-function relationships to dissect mechanisms of enzyme catalysis. Sci Adv (2022)

Release Date

2022-11-09

Peptides

Steroid Delta-isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Steroid Delta-isomerase