SMTL ID : 4c3y.1 (1 other biounit)

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 35 residues within 4Å: Chain A: V.33, G.34, S.35, G.36, L.56, E.57, K.58, T.59, G.63, G.64, T.65, S.66, Y.68, S.69, G.70, A.71, S.72, L.173, S.213, V.214, L.215, A.249, G.250, M.272, A.277, N.278, D.281, W.300, L.467, G.496, N.497, G.511, P.513, L.514 Ligands: ANB.4 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:L.173, A:M.272, A:L.467, A:L.467 Hydrogen bonds: A:G.34, A:S.35, A:S.35, A:G.36, A:K.58, A:G.63, A:T.65, A:T.65, A:S.66, A:G.70, A:A.71, A:S.72, A:S.72, A:L.215, A:L.215, A:N.278, A:D.281, A:L.467, A:N.497, A:N.497, A:G.511, A:L.514 Water bridges: A:G.37, A:G.37, A:G.38, A:E.57, A:K.58, A:G.64, A:G.250, A:G.250, A:G.251 FAD.5: 38 residues within 4Å: Chain B: V.33, G.34, S.35, G.36, L.56, E.57, K.58, T.59, G.63, G.64, T.65, S.66, Y.68, S.69, G.70, A.71, S.72, L.173, S.213, V.214, L.215, A.248, A.249, G.250, M.272, A.277, N.278, D.281, W.300, L.467, G.496, N.497, Y.507, G.511, V.512, P.513, L.514 Ligands: ANB.7 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:L.173, B:M.272, B:L.467, B:L.467 Hydrogen bonds: B:G.34, B:S.35, B:S.35, B:G.36, B:K.58, B:K.58, B:G.63, B:T.65, B:S.66, B:S.66, B:G.70, B:A.71, B:S.72, B:S.72, B:L.215, B:L.215, B:G.250, B:N.278, B:L.467, B:N.497, B:N.497, B:G.511, B:L.514 Water bridges: B:G.37, B:T.59, B:G.251, B:D.281, B:T.498 FAD.8: 39 residues within 4Å: Chain C: V.33, G.34, S.35, G.36, L.56, E.57, K.58, T.59, G.63, G.64, T.65, S.66, Y.68, S.69, G.70, A.71, S.72, L.173, S.213, V.214, L.215, A.248, A.249, G.250, M.272, A.277, N.278, D.281, W.300, F.314, L.467, G.496, N.497, Y.507, G.511, V.512, P.513, L.514 Ligands: ANB.10 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:L.173, C:M.272, C:F.314, C:L.467, C:L.467 Hydrogen bonds: C:G.34, C:S.35, C:G.36, C:K.58, C:G.63, C:T.65, C:T.65, C:S.66, C:S.66, C:G.70, C:A.71, C:S.72, C:S.72, C:L.215, C:L.215, C:G.250, C:N.278, C:L.467, C:N.497, C:N.497, C:G.511, C:L.514 Water bridges: C:G.37, C:G.37, C:G.38, C:E.57, C:G.64, C:T.498 FAD.11: 38 residues within 4Å: Chain D: V.33, G.34, S.35, G.36, L.56, E.57, K.58, T.59, G.63, G.64, T.65, S.66, Y.68, S.69, G.70, A.71, S.72, L.173, S.213, V.214, L.215, A.248, A.249, G.250, M.272, A.277, N.278, D.281, W.300, L.467, G.496, N.497, Y.507, G.511, V.512, P.513, L.514 Ligands: ANB.13 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:L.173, D:M.272, D:L.467, D:L.467 Hydrogen bonds: D:G.34, D:S.35, D:G.36, D:K.58, D:K.58, D:G.63, D:T.65, D:S.66, D:S.66, D:G.70, D:A.71, D:S.72, D:S.72, D:L.215, D:L.215, D:N.278, D:D.281, D:L.467, D:N.497, D:N.497, D:L.514 Water bridges: D:G.37, D:G.38, D:G.64, D:S.66, D:R.170, D:G.250, D:G.250, D:G.251, D:G.251

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

NA.2: 8 residues within 4Å: Chain A: D.174, Q.175, T.178, Q.180 Chain B: D.174, Q.175, T.178, Q.180 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.174, A:Q.180, B:T.178, B:Q.180 NA.9: 8 residues within 4Å: Chain C: D.174, Q.175, T.178, Q.180 Chain D: D.174, Q.175, T.178, Q.180 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.180, D:T.178, D:Q.180, D:Q.180

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

PG4.3: 9 residues within 4Å: Chain A: P.159, A.166, G.167, H.182, A.183, P.184, G.185 Chain B: R.319, E.365 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.319 Water bridges: B:R.319, B:N.376 PG4.6: 9 residues within 4Å: Chain A: I.372 Chain B: P.159, A.166, H.182, A.183, P.184, G.185, M.187 Ligands: ANB.4 No protein-ligand interaction detected (PLIP) PG4.12: 9 residues within 4Å: Chain C: R.319 Chain D: P.159, G.163, A.166, G.167, H.182, A.183, P.184, G.185 No protein-ligand interaction detected (PLIP)

4 x ANB: ANDROSTA-1,4-DIENE-3,17-DIONE(Non-covalent)

ANB.4: 11 residues within 4Å: Chain A: S.72, F.136, Y.139, F.314, Y.338, Y.507, P.510, G.511 Chain B: P.184 Ligands: FAD.1, PG4.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.136, A:F.136, A:Y.338 Hydrogen bonds: A:Y.338, A:G.511 ANB.7: 12 residues within 4Å: Chain A: P.184 Chain B: S.72, F.136, Y.139, F.314, V.316, Y.338, I.374, Y.507, P.510, G.511 Ligands: FAD.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.136, B:F.136, B:V.316, B:Y.338, B:I.374 Hydrogen bonds: B:G.511 Water bridges: B:R.191 ANB.10: 12 residues within 4Å: Chain C: S.72, F.136, Y.139, F.314, V.316, Y.338, I.374, Y.507, P.510, G.511 Chain D: P.184 Ligands: FAD.8 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.136, C:F.136, C:V.316, C:Y.338, C:I.374, C:P.510 Hydrogen bonds: C:Y.338, C:G.511 ANB.13: 11 residues within 4Å: Chain C: P.184 Chain D: S.72, F.136, Y.139, F.314, Y.338, I.374, Y.507, P.510, G.511 Ligands: FAD.11 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.136, D:F.136, D:F.314, D:Y.338, D:I.374 Hydrogen bonds: D:G.511

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohman, A. et al., Crystal Structure and Site-Directed Mutagenesis of 3-Ketosteroid Delta1-Dehydrogenase from Rhodococcus Erythropolis Sq1 Explain its Catalytic Mechanism. J.Biol.Chem. (2013)

Release Date

2013-11-06

Peptides

3-KETOSTEROID DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-KETOSTEROID DEHYDROGENASE

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