SMTL ID : 3gd4.1 (2 other biounits)

Crystal structure of the reduced, NAD-bound form of murine apoptosis inducing factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.35, G.36, G.37, G.38, T.39, A.40, V.60, S.61, E.62, D.63, R.70, P.71, L.73, S.74, K.129, K.130, V.131, A.157, T.158, G.159, G.160, F.182, R.183, L.209, N.301, L.304, G.335, D.336, E.351, H.352, H.353, A.356, F.380, W.381 Ligands: NAD.2 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:R.70, A:L.73, A:F.182, A:L.209 Hydrogen bonds: A:G.36, A:G.37, A:T.39, A:T.39, A:A.40, A:A.41, A:E.62, A:E.62, A:R.70, A:V.131, A:V.131, A:G.160, A:R.183, A:D.336, A:E.351, A:H.352, A:H.353, A:W.381 Water bridges: A:G.37, A:G.38, A:T.39, A:E.62, A:E.62, A:D.63, A:G.159, A:A.337, A:H.352, A:H.353, A:D.354 Salt bridges: A:R.70, A:R.183 FAD.3: 36 residues within 4Å: Chain B: I.35, G.36, G.37, G.38, T.39, A.40, A.41, V.60, S.61, E.62, R.70, P.71, L.73, S.74, K.129, K.130, V.131, A.157, T.158, G.159, G.160, F.182, R.183, L.209, E.212, N.301, L.304, G.335, D.336, E.351, H.352, H.353, A.356, F.380, W.381 Ligands: NAD.4 35 PLIP interactions: 35 interactions with chain B Hydrophobic interactions: B:R.70, B:L.73, B:F.182, B:L.209 Hydrogen bonds: B:G.37, B:T.39, B:T.39, B:A.40, B:A.41, B:E.62, B:E.62, B:R.70, B:V.131, B:V.131, B:G.160, B:R.183, B:D.336, B:E.351, B:H.353, B:D.354, B:W.381 Water bridges: B:G.37, B:G.38, B:T.39, B:E.62, B:D.63, B:D.63, B:D.63, B:R.70, B:R.70, B:G.159, B:D.336, B:A.337 Salt bridges: B:R.70, B:R.183

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 24 residues within 4Å: Chain A: S.74, L.165, R.183, I.204, G.205, G.206, G.207, F.208, L.209, G.210, E.212, F.232, P.233, E.234, K.240, A.295, V.296, G.297, L.298, E.351, H.352, W.381, S.382 Ligands: FAD.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.208, A:L.209 Hydrogen bonds: A:R.183, A:G.206, A:G.207, A:F.208, A:L.209, A:G.210, A:E.212, A:E.234, A:A.295, A:G.297, A:E.351, A:H.352 Water bridges: A:K.240, A:K.240, A:K.240, A:V.296, A:V.296, A:V.296, A:L.298, A:L.298, A:D.383 Salt bridges: A:K.240 NAD.4: 21 residues within 4Å: Chain B: L.165, R.183, G.206, G.207, F.208, L.209, G.210, E.212, F.232, P.233, E.234, K.240, A.295, V.296, G.297, L.298, E.351, H.352, W.381, S.382 Ligands: FAD.3 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.208 Hydrogen bonds: B:G.206, B:G.207, B:F.208, B:L.209, B:G.210, B:E.234, B:A.295, B:G.297, B:W.381 Water bridges: B:R.183, B:G.206, B:M.238, B:K.240, B:V.296, B:L.298, B:E.351, B:H.352, B:D.383 Salt bridges: B:K.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I.F., Redox-linked conformational dynamics in apoptosis-inducing factor. J.Mol.Biol. (2009)

Release Date

2009-05-19

Peptides

Apoptosis-inducing factor 1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Apoptosis-inducing factor 1, mitochondrial

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