SMTL ID : 3pfd.1 (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 Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

FDA.1: 33 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 Chain B: R.281, Q.283, F.284, R.286, V.288, N.291, V.294, Q.350, L.351, G.353, G.354 Chain D: Q.292 Ligands: IOD.26, IOD.32 31 PLIP interactions: 21 interactions with chain A, 9 interactions with chain B, 1 interactions with chain D 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, B:R.286, B:N.291, B:Q.350, B:G.354, D:Q.292 Water bridges: A:S.139, A:G.144, B:R.281, B:R.281, B:Y.355 Salt bridges: B:R.281, B:R.281 FDA.33: 32 residues within 4Å: Chain A: R.281, Q.283, F.284, R.286, V.288, N.291, V.294, Q.350, L.351, G.353, G.354 Chain B: Y.136, 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 Chain C: Q.292 Ligands: IOD.34, IOD.41 34 PLIP interactions: 21 interactions with chain B, 12 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:W.169, B:W.169, B:K.214, B:I.217, B:T.222, B:I.372, B:Y.376 Hydrogen bonds: B:Y.136, B:L.138, B:S.139, B:S.139, B:S.139, B:S.145, B:S.145, B:T.171, B:T.171, B:E.377, B:T.379, A:R.286, A:N.291, A:Q.350, A:G.354, C:Q.292 Water bridges: B:Y.136, B:S.139, B:G.144, A:R.281, A:R.281, A:R.281, A:R.281, A:Y.355, A:Y.355 Salt bridges: A:R.281, A:R.281 FDA.62: 31 residues within 4Å: Chain B: Q.292 Chain C: 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, Y.376, E.377, T.379, Q.381 Chain D: R.281, Q.283, F.284, R.286, V.288, N.291, V.294, Q.350, L.351, G.353, G.354 Ligands: IOD.66, IOD.68 28 PLIP interactions: 8 interactions with chain D, 19 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:R.286, D:N.291, D:Q.350, D:G.354, C:Y.136, C:L.138, C:S.139, C:S.139, C:S.139, C:S.145, C:S.145, C:T.171, C:T.171, C:E.377, C:T.379, B:Q.292 Water bridges: D:R.281, D:R.281, C:T.379 Salt bridges: D:R.281, D:R.281 Hydrophobic interactions: C:W.169, C:W.169, C:K.214, C:I.217, C:T.222, C:I.372, C:Y.376 FDA.85: 33 residues within 4Å: Chain A: Q.292 Chain C: R.281, Q.283, F.284, R.286, V.288, N.291, V.294, Q.350, L.351, G.353, G.354 Chain D: 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.86, IOD.105 32 PLIP interactions: 21 interactions with chain D, 10 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:W.169, D:W.169, D:K.214, D:I.217, D:T.222, D:I.372, D:Y.376 Hydrogen bonds: D:Y.136, D:L.138, D:S.139, D:S.139, D:S.139, D:S.145, D:S.145, D:T.171, D:T.171, D:T.171, D:E.377, D:T.379, D:T.379, C:R.286, C:N.291, C:Q.350, C:G.354, A:Q.292 Water bridges: D:Y.136, C:R.281, C:R.281, C:R.281, C:R.281 Salt bridges: C:R.281, C:R.281

109 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: 5 residues within 4Å: Chain A: S.289, D.290, Q.295 Chain D: L.392 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: 3 residues within 4Å: Chain A: R.389 Chain D: Q.292 Ligands: FDA.1 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain A: D.300, K.304 Chain D: R.384 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain A: K.304 Chain D: K.304, F.336 Ligand excluded by PLIP IOD.29: 3 residues within 4Å: Chain A: R.318, F.328 Chain D: E.306 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: 3 residues within 4Å: Chain A: Q.381, R.384 Chain D: F.296 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain A: E.377 Ligands: FDA.1 Ligand excluded by PLIP IOD.34: 3 residues within 4Å: Chain B: R.389 Chain C: Q.292 Ligands: FDA.33 Ligand excluded by PLIP IOD.35: 4 residues within 4Å: Chain A: M.297 Chain B: Q.381, R.384 Chain C: F.296 Ligand excluded by PLIP IOD.36: 5 residues within 4Å: Chain B: D.339, Q.374, N.380, Q.381, R.384 Ligand excluded by PLIP IOD.37: 2 residues within 4Å: Chain B: K.304 Chain C: K.304 Ligand excluded by PLIP IOD.38: 3 residues within 4Å: Chain B: D.300, K.304 Chain C: R.384 Ligand excluded by PLIP IOD.39: 3 residues within 4Å: Chain B: D.290, Q.295 Ligands: IOD.40 Ligand excluded by PLIP IOD.40: 5 residues within 4Å: Chain B: S.289, D.290, Q.295 Chain C: L.392 Ligands: IOD.39 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain B: E.377 Ligands: FDA.33 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain B: A.49, R.213, K.214 Ligand excluded by PLIP IOD.43: 3 residues within 4Å: Chain B: H.23, I.24, R.27 Ligand excluded by PLIP IOD.44: 1 residues within 4Å: Chain B: E.28 Ligand excluded by PLIP IOD.45: 3 residues within 4Å: Chain B: E.22, H.23 Ligands: IOD.46 Ligand excluded by PLIP IOD.46: 3 residues within 4Å: Chain B: A.78, D.79 Ligands: IOD.45 Ligand excluded by PLIP IOD.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.48: 1 residues within 4Å: Chain B: R.365 Ligand excluded by PLIP IOD.49: 2 residues within 4Å: Chain B: E.44, E.47 Ligand excluded by PLIP IOD.50: 1 residues within 4Å: Chain B: E.44 Ligand excluded by PLIP IOD.51: 1 residues within 4Å: Chain B: K.211 Ligand excluded by PLIP IOD.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.53: 4 residues within 4Å: Chain B: K.105, H.254, A.316 Ligands: IOD.54 Ligand excluded by PLIP IOD.54: 5 residues within 4Å: Chain B: S.80, K.105, H.254 Ligands: IOD.53, IOD.55 Ligand excluded by PLIP IOD.55: 3 residues within 4Å: Chain B: K.105, M.109 Ligands: IOD.54 Ligand excluded by PLIP IOD.56: 3 residues within 4Å: Chain B: R.141, S.166, K.167 Ligand excluded by PLIP IOD.57: 4 residues within 4Å: Chain B: T.185, D.186, P.241, G.242 Ligand excluded by PLIP IOD.58: 3 residues within 4Å: Chain B: D.160, R.231, P.233 Ligand excluded by PLIP IOD.59: 1 residues within 4Å: Chain B: Y.277 Ligand excluded by PLIP IOD.60: 2 residues within 4Å: Chain B: R.318 Chain C: E.306 Ligand excluded by PLIP IOD.61: 1 residues within 4Å: Chain B: R.318 Ligand excluded by PLIP IOD.63: 3 residues within 4Å: Chain B: R.384 Chain C: D.300, K.304 Ligand excluded by PLIP IOD.64: 4 residues within 4Å: Chain B: F.296 Chain C: Q.381, R.384 Chain D: M.297 Ligand excluded by PLIP IOD.65: 5 residues within 4Å: Chain C: D.339, Q.374, N.380, Q.381, R.384 Ligand excluded by PLIP IOD.66: 4 residues within 4Å: Chain B: Q.292 Chain C: R.389 Chain D: R.286 Ligands: FDA.62 Ligand excluded by PLIP IOD.67: 3 residues within 4Å: Chain C: E.142 Chain D: R.281, K.282 Ligand excluded by PLIP IOD.68: 2 residues within 4Å: Chain C: E.377 Ligands: FDA.62 Ligand excluded by PLIP IOD.69: 3 residues within 4Å: Chain B: E.306 Chain C: R.318, F.328 Ligand excluded by PLIP IOD.70: 3 residues within 4Å: Chain C: H.23, I.24, R.27 Ligand excluded by PLIP IOD.71: 1 residues within 4Å: Chain C: E.28 Ligand excluded by PLIP IOD.72: 1 residues within 4Å: Chain C: H.23 Ligand excluded by PLIP IOD.73: 1 residues within 4Å: Chain C: R.365 Ligand excluded by PLIP IOD.74: 1 residues within 4Å: Chain C: Y.277 Ligand excluded by PLIP IOD.75: 2 residues within 4Å: Chain C: K.282, G.285 Ligand excluded by PLIP IOD.76: 3 residues within 4Å: Chain C: A.49, R.213, K.214 Ligand excluded by PLIP IOD.77: 3 residues within 4Å: Chain C: K.105, M.109 Ligands: IOD.78 Ligand excluded by PLIP IOD.78: 5 residues within 4Å: Chain C: S.80, K.105, H.254 Ligands: IOD.77, IOD.79 Ligand excluded by PLIP IOD.79: 5 residues within 4Å: Chain C: K.105, H.254, P.257, A.316 Ligands: IOD.78 Ligand excluded by PLIP IOD.80: 1 residues within 4Å: Chain C: T.243 Ligand excluded by PLIP IOD.81: 3 residues within 4Å: Chain C: R.141, S.166, K.167 Ligand excluded by PLIP IOD.82: 3 residues within 4Å: Chain C: T.185, D.186, G.242 Ligand excluded by PLIP IOD.83: 2 residues within 4Å: Chain C: S.289, D.290 Ligand excluded by PLIP IOD.84: 1 residues within 4Å: Chain C: R.389 Ligand excluded by PLIP IOD.86: 4 residues within 4Å: Chain A: Q.292 Chain C: R.286 Chain D: R.389 Ligands: FDA.85 Ligand excluded by PLIP IOD.87: 2 residues within 4Å: Chain D: V.386, R.389 Ligand excluded by PLIP IOD.88: 2 residues within 4Å: Chain D: S.289, D.290 Ligand excluded by PLIP IOD.89: 1 residues within 4Å: Chain D: Y.277 Ligand excluded by PLIP IOD.90: 2 residues within 4Å: Chain D: F.361, P.362 Ligand excluded by PLIP IOD.91: 4 residues within 4Å: Chain A: F.296 Chain C: M.297 Chain D: Q.381, R.384 Ligand excluded by PLIP IOD.92: 5 residues within 4Å: Chain D: D.339, Q.374, N.380, Q.381, R.384 Ligand excluded by PLIP IOD.93: 3 residues within 4Å: Chain A: E.306 Chain D: R.318, F.328 Ligand excluded by PLIP IOD.94: 1 residues within 4Å: Chain D: R.27 Ligand excluded by PLIP IOD.95: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.96: 3 residues within 4Å: Chain A: R.384 Chain D: D.300, K.304 Ligand excluded by PLIP IOD.97: 3 residues within 4Å: Chain C: R.281, K.282 Chain D: E.142 Ligand excluded by PLIP IOD.98: 2 residues within 4Å: Chain D: E.22 Ligands: IOD.99 Ligand excluded by PLIP IOD.99: 3 residues within 4Å: Chain D: A.78, D.79 Ligands: IOD.98 Ligand excluded by PLIP IOD.100: 3 residues within 4Å: Chain D: A.49, R.213, K.214 Ligand excluded by PLIP IOD.101: 1 residues within 4Å: Chain D: K.211 Ligand excluded by PLIP IOD.102: 3 residues within 4Å: Chain D: K.105, M.109 Ligands: IOD.103 Ligand excluded by PLIP IOD.103: 3 residues within 4Å: Chain D: K.105, H.254 Ligands: IOD.102 Ligand excluded by PLIP IOD.104: 4 residues within 4Å: Chain D: K.105, H.254, P.257, A.316 Ligand excluded by PLIP IOD.105: 2 residues within 4Å: Chain D: E.377 Ligands: FDA.85 Ligand excluded by PLIP IOD.106: 2 residues within 4Å: Chain D: A.126, W.178 Ligand excluded by PLIP IOD.107: 4 residues within 4Å: Chain D: E.140, R.141, S.166, K.167 Ligand excluded by PLIP IOD.108: 2 residues within 4Å: Chain D: G.234, D.235 Ligand excluded by PLIP IOD.109: 4 residues within 4Å: Chain D: D.160, R.231, I.232, P.233 Ligand excluded by PLIP IOD.110: 1 residues within 4Å: Chain D: V.155 Ligand excluded by PLIP IOD.111: 3 residues within 4Å: Chain D: T.185, D.186, G.242 Ligand excluded by PLIP IOD.112: 2 residues within 4Å: Chain D: K.282, G.285 Ligand excluded by PLIP IOD.113: 2 residues within 4Å: Chain D: E.44, E.47 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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Acyl-CoA dehydrogenase

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