SMTL ID : 4c3x.2 (1 other biounit)

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

6 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 9 residues within 4Å: Chain A: R.134, D.156, I.188 Chain B: D.158, P.159, P.184, G.185, P.186 Ligands: PG4.11 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.158, B:G.185, A:R.134, A:R.134 Water bridges: B:D.158, A:R.134, A:D.156, A:G.189, A:G.189 GLC-FRU.2: 8 residues within 4Å: Chain A: D.158, P.159, P.184, G.185, P.186 Chain B: R.134, D.156, I.188 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:R.134, B:D.156, B:G.189, B:G.189 Hydrogen bonds: A:D.158, B:R.134, B:R.134 GLC-FRU.3: 8 residues within 4Å: Chain B: L.383, G.390, A.391, D.392, E.396, K.400, P.456, Y.458 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.390, B:G.390, B:Y.458, B:D.392, B:E.396, B:K.400 GLC-FRU.4: 9 residues within 4Å: Chain C: R.134, D.156, I.188 Chain D: D.158, P.159, P.184, G.185, P.186 Ligands: PG4.20 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:D.158, D:G.185, C:R.134, C:R.134 Water bridges: C:D.156, C:G.189, C:G.189 GLC-FRU.5: 10 residues within 4Å: Chain C: D.158, P.159, P.184, G.185, P.186 Chain D: R.134, D.156, I.188 Ligands: PG4.24, PG4.25 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Water bridges: D:R.134, D:D.156, D:G.189, D:G.189 Hydrogen bonds: C:D.158, C:G.185, D:R.134, D:R.134 GLC-FRU.6: 8 residues within 4Å: Chain D: L.383, G.390, A.391, D.392, E.396, K.400, P.456, Y.458 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.390, D:G.390, D:Y.458, D:D.392, D:E.396, D:K.400

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

FAD.7: 40 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.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: CL.9, PG4.10 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.173, A:M.272, A:F.314, A:L.467, A:L.467 Hydrogen bonds: A:G.34, A:G.36, A:K.58, A:G.63, A:T.65, A:T.65, A:S.66, A:S.66, A:G.70, A:S.72, A:S.72, A:L.215, A:L.215, A:G.250, A:N.278, A:L.467, A:N.497, A:N.497, A:G.511, A:L.514 Water bridges: A:G.64, A:G.251, A:G.251, A:T.498 FAD.13: 40 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, F.314, L.467, G.496, N.497, Y.507, G.511, V.512, P.513, L.514 Ligands: CL.14, PG4.15 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:L.173, B:M.272, B:F.314, B:L.467, B:L.467 Hydrogen bonds: B:G.34, B:S.35, B:G.36, B:K.58, B:G.63, B:T.65, B:S.66, B:S.66, B:G.70, B:S.72, B:S.72, B:L.215, B:L.215, B:G.250, B:N.278, B:D.281, B:L.467, B:N.497, B:N.497, B:G.511, B:L.514 Water bridges: B:G.38, B:G.38, B:E.57, B:G.64, B:S.66, B:G.251, B:T.498 FAD.17: 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.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: CL.19, PG4.20 32 PLIP interactions: 32 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:S.72, C:S.72, C:L.215, C:L.215, C:G.250, C:N.278, C:D.281, C:L.467, C:N.497, C:N.497, C:Y.507, C:G.511, C:L.514 Water bridges: C:G.37, C:G.64, C:G.251, C:T.498 FAD.22: 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.249, G.250, M.272, A.277, N.278, D.281, F.314, L.467, G.496, N.497, Y.507, G.511, V.512, P.513, L.514 Ligands: CL.23, PG4.24 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:L.173, D:M.272, D:F.314, D:L.467, D:L.467 Hydrogen bonds: D:G.34, D:S.35, D:G.36, D:K.58, D:G.63, D:T.65, D:S.66, D:S.66, D:G.70, D:S.72, D:S.72, D:L.215, D:L.215, D:G.250, D:N.278, D:L.467, D:N.497, D:N.497, D:Y.507, D:G.511, D:L.514 Water bridges: D:G.37, D:G.38, D:G.38, D:E.57, D:G.64, D:G.251, D:G.251, D:T.498

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

NA.8: 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 B, 2 interactions with chain A Hydrogen bonds: B:T.178, B:Q.180, A:T.178, A:Q.180 NA.18: 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: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.178, D:Q.180, C:Q.180, C:Q.180

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

CL.9: 6 residues within 4Å: Chain A: Y.338, Y.507, P.510, G.511 Ligands: FAD.7, PG4.10 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: Y.338, Y.507, P.510, G.511 Ligands: FAD.13, PG4.15 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain C: Y.338, Y.507, P.510, G.511 Ligands: FAD.17, PG4.20 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain D: Y.338, Y.507, P.510, G.511 Ligands: FAD.22, PG4.24 Ligand excluded by PLIP

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

PG4.10: 10 residues within 4Å: Chain A: G.70, S.72, F.136, F.314, V.316, I.374 Chain B: P.184 Ligands: FAD.7, CL.9, PG4.11 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.70, A:N.153, A:N.153 PG4.11: 8 residues within 4Å: Chain A: F.136, I.372, F.437, F.438 Chain B: A.160, P.184 Ligands: GLC-FRU.1, PG4.10 No protein-ligand interaction detected (PLIP) PG4.12: 4 residues within 4Å: Chain A: G.386, A.399, K.400, R.461 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.399 Water bridges: A:R.461 PG4.15: 7 residues within 4Å: Chain B: G.70, S.72, F.136, F.314, I.374 Ligands: FAD.13, CL.14 No protein-ligand interaction detected (PLIP) PG4.16: 8 residues within 4Å: Chain A: P.159, G.163, A.166, H.182, A.183, P.184, G.185 Chain B: R.319 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.159 Water bridges: B:R.319, B:N.376 PG4.20: 7 residues within 4Å: Chain C: S.72, F.136, V.316 Chain D: P.184 Ligands: GLC-FRU.4, FAD.17, CL.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.72 Water bridges: C:N.153 PG4.21: 7 residues within 4Å: Chain D: P.159, A.166, G.167, H.182, A.183, P.184, G.185 1 PLIP interactions: 1 interactions with chain D Water bridges: D:A.166 PG4.24: 12 residues within 4Å: Chain C: P.184 Chain D: G.70, S.72, F.136, F.314, Y.338, I.372, I.374 Ligands: GLC-FRU.5, FAD.22, CL.23, PG4.25 No protein-ligand interaction detected (PLIP) PG4.25: 8 residues within 4Å: Chain C: P.159, A.160, P.184 Chain D: F.136, I.372, F.438 Ligands: GLC-FRU.5, PG4.24 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.319, D:R.319

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
E

B
F

C
G

D
H

3-KETOSTEROID DEHYDROGENASE

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