SMTL ID : 6wy9.1

Tcur3481-Tcur3483 steroid ACAD G363A variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.1: 33 residues within 4Å: Chain A: I.144, G.145, Y.146, T.147, G.152, T.153, F.177, S.179, T.222, M.226, V.228, V.379, F.382, A.383, V.386, E.388, V.389 Chain B: R.249, Q.251, F.252, L.256, F.259, A.261, V.262, H.317, L.318, H.319, G.320, G.321, V.324 Chain D: Q.260 Ligands: GOL.5, GOL.6 28 PLIP interactions: 17 interactions with chain A, 10 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:F.177, A:V.379, A:F.382, B:V.324 Hydrogen bonds: A:I.144, A:Y.146, A:T.147, A:T.147, A:T.147, A:T.147, A:T.153, A:T.153, A:S.179, A:S.179, A:E.388, B:Q.251, B:H.317, B:G.320, B:G.321, D:Q.260 Water bridges: A:T.147, A:G.152, A:D.392, B:R.249, B:R.249, B:I.322 Salt bridges: B:R.249, B:R.249 FDA.18: 33 residues within 4Å: Chain B: Q.260 Chain C: I.144, G.145, Y.146, T.147, G.152, T.153, F.177, S.179, T.222, M.226, V.228, V.379, F.382, A.383, V.386, E.388, V.389 Chain D: R.249, Q.251, F.252, L.256, F.259, A.261, V.262, H.317, L.318, H.319, G.320, G.321, V.324 Ligands: GOL.22, GOL.23 28 PLIP interactions: 17 interactions with chain C, 10 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: C:F.177, C:V.379, C:F.382, D:V.324 Hydrogen bonds: C:I.144, C:Y.146, C:T.147, C:T.147, C:T.147, C:T.147, C:T.153, C:T.153, C:S.179, C:S.179, C:E.388, D:Q.251, D:H.317, D:G.320, D:G.321, B:Q.260 Water bridges: C:T.147, C:G.152, C:D.392, D:R.249, D:R.249, D:I.322 Salt bridges: D:R.249, D:R.249

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 10 residues within 4Å: Chain A: I.273, R.274, W.276, E.277, Y.302, L.305, E.306, R.309, L.310 Chain D: Q.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.277, A:E.306, A:R.309, A:R.309 1PE.19: 10 residues within 4Å: Chain B: Q.282 Chain C: I.273, R.274, W.276, E.277, Y.302, L.305, E.306, R.309, L.310 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.277, C:E.306, C:R.309, C:R.309

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: E.338, I.341, T.381, N.387 Chain B: Q.265, H.313, H.317 Ligands: GOL.14 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: A.156, S.157, R.192, P.195, A.197, K.199 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: I.144, Y.146, L.258, E.261, A.383, G.384 Ligands: FDA.1, GOL.6 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: G.152, T.153, L.155, L.258, G.385, V.386 Ligands: FDA.1, GOL.5 Ligand excluded by PLIP GOL.7: 9 residues within 4Å: Chain A: D.297, R.300, D.342, R.345, T.346 Chain B: E.306, A.347, S.348 Ligands: GOL.16 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: Q.291, W.293 Chain B: D.130, A.349, Q.352, R.353, D.356 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: Q.101, R.102, R.271, R.274, L.275, D.278, Q.369 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: R.50, G.53, E.54, R.271, P.359, Q.369, Q.372, L.373, Q.376 Ligand excluded by PLIP GOL.12: 10 residues within 4Å: Chain B: D.268, I.271, E.272, R.314 Chain C: K.304, A.334, Y.335, E.338, R.391 Ligands: GOL.13 Ligand excluded by PLIP GOL.13: 9 residues within 4Å: Chain B: E.272, W.302, W.303, E.306, N.310, R.314 Chain C: K.304, Y.335 Ligands: GOL.12 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: R.345 Chain B: E.306, N.310, H.313, R.314 Ligands: GOL.3 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: W.88, S.194, D.196, L.227, W.336, Q.339, I.340 Ligand excluded by PLIP GOL.16: 11 residues within 4Å: Chain A: R.345, T.348, G.349 Chain B: D.305, L.309, K.338, S.341, G.342, G.346, A.347 Ligands: GOL.7 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain C: E.338, I.341, T.381, N.387 Chain D: Q.265, H.313, H.317 Ligands: GOL.31 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain C: A.156, S.157, R.192, P.195, A.197, K.199 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain C: I.144, Y.146, L.258, E.261, A.383, G.384 Ligands: FDA.18, GOL.23 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain C: G.152, T.153, L.155, L.258, G.385, V.386 Ligands: FDA.18, GOL.22 Ligand excluded by PLIP GOL.24: 9 residues within 4Å: Chain C: D.297, R.300, D.342, R.345, T.346 Chain D: E.306, A.347, S.348 Ligands: GOL.33 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain C: Q.291, W.293 Chain D: D.130, A.349, Q.352, R.353, D.356 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain C: Q.101, R.102, R.271, R.274, L.275, D.278, Q.369 Ligand excluded by PLIP GOL.27: 9 residues within 4Å: Chain C: R.50, G.53, E.54, R.271, P.359, Q.369, Q.372, L.373, Q.376 Ligand excluded by PLIP GOL.29: 10 residues within 4Å: Chain A: K.304, A.334, Y.335, E.338, R.391 Chain D: D.268, I.271, E.272, R.314 Ligands: GOL.30 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain A: K.304, Y.335 Chain D: E.272, W.302, W.303, E.306, N.310, R.314 Ligands: GOL.29 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: R.345 Chain D: E.306, N.310, H.313, R.314 Ligands: GOL.20 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain D: W.88, S.194, D.196, L.227, W.336, Q.339, I.340 Ligand excluded by PLIP GOL.33: 11 residues within 4Å: Chain C: R.345, T.348, G.349 Chain D: D.305, L.309, K.338, S.341, G.342, G.346, A.347 Ligands: GOL.24 Ligand excluded by PLIP

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

CL.11: 4 residues within 4Å: Chain A: V.57, P.108, V.110, T.111 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain C: V.57, P.108, V.110, T.111 Ligand excluded by PLIP CL.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stirling, A.J. et al., A Key Glycine in Bacterial Steroid-Degrading Acyl-CoA Dehydrogenases Allows Flavin-Ring Repositioning and Modulates Substrate Side Chain Specificity. Biochemistry (2020)

Release Date

2020-10-28

Peptides

Acyl-CoA dehydrogenase domain protein Tcur3483: AC
Acyl-CoA dehydrogenase domain protein Tcur3481: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Acyl-CoA dehydrogenase domain protein Tcur3483

Acyl-CoA dehydrogenase domain protein Tcur3481

Related Entries With Identical Sequence