SMTL ID : 3pfd.2 (4 other biounits)

Crystal structure of an Acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to reduced flavin adenine dinucleotide solved by combined iodide ion SAD MR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

FDA.1: 21 residues within 4Å: Chain A: Y.136, A.137, L.138, S.139, G.144, S.145, W.169, I.170, T.171, K.214, I.217, T.222, I.372, I.375, Y.376, E.377, T.379, Q.381, I.382 Ligands: IOD.26, IOD.32 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.169, A:W.169, A:K.214, A:I.217, A:T.222, A:I.372, A:Y.376 Hydrogen bonds: A:Y.136, A:L.138, A:S.139, A:S.139, A:S.145, A:S.145, A:T.171, A:T.171, A:T.171, A:E.377, A:T.379, A:T.379 Water bridges: A:S.139, A:G.144, A:W.169

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

IOD.2: 2 residues within 4Å: Chain A: H.23 Ligands: IOD.3 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: A.78, D.79 Ligands: IOD.2 Ligand excluded by PLIP IOD.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: I.24, R.27 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: E.28 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: E.44 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain A: A.49, R.213, K.214, K.218 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: F.51 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: K.105 Ligands: IOD.11 Ligand excluded by PLIP IOD.11: 5 residues within 4Å: Chain A: S.80, K.105, H.254 Ligands: IOD.10, IOD.12 Ligand excluded by PLIP IOD.12: 5 residues within 4Å: Chain A: K.105, H.254, P.257, A.316 Ligands: IOD.11 Ligand excluded by PLIP IOD.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: R.365 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: Y.277 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: A.126, S.129 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: E.140, R.141, S.166, K.167 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: R.153, I.162 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: D.160, P.233 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain A: R.231 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: T.185, D.186, G.242 Ligand excluded by PLIP IOD.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain A: G.239, E.240, T.243 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain A: S.289, D.290, Q.295 Ligands: IOD.25 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain A: D.290, Q.295 Ligands: IOD.24 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: R.389 Ligands: FDA.1 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: D.300, K.304 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain A: K.304 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: R.318, F.328 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: D.339, Q.374, Q.381, R.384 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain A: Q.381, R.384 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain A: E.377 Ligands: FDA.1 Ligand excluded by PLIP

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.GENOM. (2011)

Release Date

2010-11-10

Peptides

Acyl-CoA dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Acyl-CoA dehydrogenase

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