SMTL ID : 3oib.2 (2 other biounits)

Crystal structure of a putative ACYL-COA Dehydrogenase from mycobacterium smegmatis, Iodide soak

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 2 residues within 4Å: Chain A: R.321 Chain D: H.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.321 NA.19: 2 residues within 4Å: Chain B: R.321 Chain C: H.322 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:H.322 Hydrogen bonds: B:R.321 NA.36: 2 residues within 4Å: Chain B: H.322 Chain C: R.321 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.321 Water bridges: C:S.23 NA.54: 2 residues within 4Å: Chain A: H.322 Chain D: R.321 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Water bridges: A:H.322 Hydrogen bonds: D:R.321

58 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: L.62, K.65 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: R.311 Chain D: N.343, T.392 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: H.50, R.373 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: D.79, A.80, I.129 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: M.366, E.368 Chain B: R.218, D.221 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: Y.132, K.141, D.186 Ligand excluded by PLIP IOD.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: R.287, N.288 Ligand excluded by PLIP IOD.10: 5 residues within 4Å: Chain A: E.149, R.160, T.161, A.175 Ligands: IOD.14 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: E.284, W.285 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: V.261, R.264, V.338 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: A.258, A.259 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: G.151, R.160 Ligands: IOD.10 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: V.216 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: R.134, P.135 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain B: R.311 Chain C: N.343, T.392 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain B: A.49, H.50, R.373 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain B: P.59, E.61, L.62, K.65 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain B: E.51 Ligand excluded by PLIP IOD.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain B: D.79, A.80 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain B: H.169, P.241 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain A: R.218, D.221 Chain B: M.366, E.368 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain B: V.261, R.264, V.338 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain B: R.226 Ligand excluded by PLIP IOD.30: 1 residues within 4Å: Chain B: Q.327 Ligand excluded by PLIP IOD.31: 3 residues within 4Å: Chain B: P.150, G.151 Ligands: IOD.32 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain B: E.149, T.161, A.175 Ligands: IOD.31 Ligand excluded by PLIP IOD.33: 2 residues within 4Å: Chain B: E.284, W.285 Ligand excluded by PLIP IOD.37: 2 residues within 4Å: Chain C: L.62, K.65 Ligand excluded by PLIP IOD.38: 3 residues within 4Å: Chain B: N.343, T.392 Chain C: R.311 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain C: H.50, R.373 Ligand excluded by PLIP IOD.40: 3 residues within 4Å: Chain C: D.79, A.80, I.129 Ligand excluded by PLIP IOD.41: 4 residues within 4Å: Chain C: M.366, E.368 Chain D: R.218, D.221 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain C: Y.132, K.141, D.186 Ligand excluded by PLIP IOD.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.44: 2 residues within 4Å: Chain C: R.287, N.288 Ligand excluded by PLIP IOD.45: 5 residues within 4Å: Chain C: E.149, R.160, T.161, A.175 Ligands: IOD.49 Ligand excluded by PLIP IOD.46: 2 residues within 4Å: Chain C: E.284, W.285 Ligand excluded by PLIP IOD.47: 3 residues within 4Å: Chain C: V.261, R.264, V.338 Ligand excluded by PLIP IOD.48: 2 residues within 4Å: Chain C: A.258, A.259 Ligand excluded by PLIP IOD.49: 3 residues within 4Å: Chain C: G.151, R.160 Ligands: IOD.45 Ligand excluded by PLIP IOD.50: 1 residues within 4Å: Chain C: V.216 Ligand excluded by PLIP IOD.51: 2 residues within 4Å: Chain C: R.134, P.135 Ligand excluded by PLIP IOD.55: 3 residues within 4Å: Chain A: N.343, T.392 Chain D: R.311 Ligand excluded by PLIP IOD.56: 3 residues within 4Å: Chain D: A.49, H.50, R.373 Ligand excluded by PLIP IOD.57: 4 residues within 4Å: Chain D: P.59, E.61, L.62, K.65 Ligand excluded by PLIP IOD.58: 1 residues within 4Å: Chain D: E.51 Ligand excluded by PLIP IOD.59: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.60: 2 residues within 4Å: Chain D: D.79, A.80 Ligand excluded by PLIP IOD.61: 2 residues within 4Å: Chain D: H.169, P.241 Ligand excluded by PLIP IOD.62: 4 residues within 4Å: Chain C: R.218, D.221 Chain D: M.366, E.368 Ligand excluded by PLIP IOD.63: 3 residues within 4Å: Chain D: V.261, R.264, V.338 Ligand excluded by PLIP IOD.64: 1 residues within 4Å: Chain D: R.226 Ligand excluded by PLIP IOD.65: 1 residues within 4Å: Chain D: Q.327 Ligand excluded by PLIP IOD.66: 3 residues within 4Å: Chain D: P.150, G.151 Ligands: IOD.67 Ligand excluded by PLIP IOD.67: 4 residues within 4Å: Chain D: E.149, T.161, A.175 Ligands: IOD.66 Ligand excluded by PLIP IOD.68: 2 residues within 4Å: Chain D: E.284, W.285 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.17: 5 residues within 4Å: Chain A: Q.276, A.310, D.314, R.317 Chain D: L.399 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.276, A:Q.276, A:R.317, A:R.317 EDO.35: 5 residues within 4Å: Chain B: Q.276, A.310, D.314, R.317 Chain C: L.399 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.276, B:Q.276, B:R.317, B:R.317 EDO.52: 5 residues within 4Å: Chain B: L.399 Chain C: Q.276, A.310, D.314, R.317 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.276, C:Q.276, C:R.317, C:R.317 EDO.70: 5 residues within 4Å: Chain A: L.399 Chain D: Q.276, A.310, D.314, R.317 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.276, D:Q.276, D:R.317, D:R.317

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

FDA.18: 27 residues within 4Å: Chain A: I.115, L.145, A.146, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, I.380, I.383, G.385, T.387, E.389 Chain B: R.289, T.291, L.296, R.299, Q.358, L.359, G.361, G.362, M.366 Chain D: Q.300 31 PLIP interactions: 1 interactions with chain D, 22 interactions with chain A, 8 interactions with chain B Hydrogen bonds: D:Q.300, A:L.145, A:I.147, A:T.148, A:T.148, A:T.148, A:G.153, A:S.154, A:S.154, A:T.180, A:T.180, A:T.180, A:G.385, A:T.387, A:T.387, A:E.389, B:T.291, B:T.291, B:Q.358, B:G.362 Hydrophobic interactions: A:Y.178, A:K.222, A:I.380 Water bridges: A:G.152, A:D.155, A:G.386, A:G.386, B:R.289, B:M.363 Salt bridges: B:R.289, B:R.289 FDA.34: 27 residues within 4Å: Chain A: R.289, T.291, F.292, L.296, R.299, Q.358, L.359, G.361, G.362, M.366 Chain B: I.115, L.145, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, W.225, I.380, I.383, T.387, E.389 Chain C: Q.300 27 PLIP interactions: 20 interactions with chain B, 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:Y.178, B:K.222, B:W.225, B:I.380 Hydrogen bonds: B:L.145, B:I.147, B:T.148, B:T.148, B:T.148, B:G.153, B:S.154, B:S.154, B:T.180, B:T.180, B:G.385, B:T.387, A:T.291, A:T.291, A:Q.358, A:G.362, C:Q.300 Water bridges: B:Y.178, B:Y.178, B:G.386, B:G.386 Salt bridges: A:R.289, A:R.289 FDA.53: 27 residues within 4Å: Chain B: Q.300 Chain C: I.115, L.145, A.146, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, I.380, I.383, G.385, T.387, E.389 Chain D: R.289, T.291, L.296, R.299, Q.358, L.359, G.361, G.362, M.366 30 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B, 22 interactions with chain C Hydrogen bonds: D:T.291, D:T.291, D:Q.358, D:G.362, B:Q.300, C:L.145, C:I.147, C:T.148, C:T.148, C:T.148, C:G.153, C:S.154, C:S.154, C:T.180, C:T.180, C:G.385, C:T.387 Water bridges: D:R.289, C:G.152, C:D.155, C:Y.178, C:Y.178, C:T.180, C:G.386, C:G.386 Salt bridges: D:R.289, D:R.289 Hydrophobic interactions: C:Y.178, C:K.222, C:I.380 FDA.69: 27 residues within 4Å: Chain A: Q.300 Chain C: R.289, T.291, F.292, L.296, R.299, Q.358, L.359, G.361, G.362, M.366 Chain D: I.115, L.145, I.147, T.148, G.152, G.153, S.154, Y.178, I.179, T.180, K.222, W.225, I.380, I.383, T.387, E.389 29 PLIP interactions: 21 interactions with chain D, 1 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: D:Y.178, D:K.222, D:W.225, D:I.380 Hydrogen bonds: D:L.145, D:I.147, D:T.148, D:T.148, D:T.148, D:G.153, D:S.154, D:S.154, D:T.180, D:T.180, D:T.180, D:G.385, D:T.387, D:T.387, D:E.389, A:Q.300, C:T.291, C:T.291, C:Q.358, C:G.362 Water bridges: D:G.386, D:G.386, C:M.363 Salt bridges: C:R.289, C:R.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., SAD phasing using iodide ions in a high-throughput structural genomics environment. J Struct Funct Genomics (2011)

Release Date

2010-09-01

Peptides

Acyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acyl-CoA dehydrogenase

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