SMTL ID : 3t4h.1

Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(3-nitrobenzyl)-L-cysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: H.121, D.123, H.177 Ligands: MD5.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.121, A:D.123, A:H.177, H2O.7

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 11 residues within 4Å: Chain A: M.47, M.51, W.59, L.108, K.117, L.118, S.119, H.121, D.123, R.200 Ligands: MD5.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.119, A:R.200, A:R.200 Water bridges: A:S.48, A:D.125 Salt bridges: A:D.123 pi-Cation interactions: A:W.59

1 x MD5: N-(carboxycarbonyl)-S-(3-nitrobenzyl)-L-cysteine(Non-covalent)

MD5.3: 22 residues within 4Å: Chain A: L.108, N.110, Y.112, L.118, H.121, D.123, I.133, S.135, F.144, F.146, W.168, S.172, R.173, F.175, H.177, I.179, R.194, N.196, T.198, R.200 Ligands: FE.1, EPE.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.133, A:F.144, A:W.168, A:W.168 Hydrogen bonds: A:N.110, A:Y.112 Water bridges: A:N.110, A:R.194, A:R.200, A:R.200 Salt bridges: A:H.121, A:R.194, A:R.200 pi-Stacking: A:W.168, A:H.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woon, E.C. et al., Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic Acid demethylase. J.Med.Chem. (2012)

Release Date

2012-03-07

Peptides

Alpha-ketoglutarate-dependent dioxygenase AlkB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Alpha-ketoglutarate-dependent dioxygenase AlkB

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