SMTL ID : 4qkb.4 (3 other biounits)

Crystal structure of seleno-methionine labelled human ALKBH7 in complex with alpha-ketoglutarate and Mn(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

7 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.106, D.108, H.162 Ligands: AKG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.106, A:D.108, A:H.162 MN.3: 3 residues within 4Å: Chain A: E.47, E.60 Chain B: H.50 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.47, A:E.60, B:H.50 MN.4: 1 residues within 4Å: Chain A: E.174 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.174 MN.5: 4 residues within 4Å: Chain B: H.106, D.108, H.162 Ligands: AKG.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.106, B:D.108, B:D.108, B:H.162 MN.7: 3 residues within 4Å: Chain B: E.47, E.60 Chain C: H.50 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.50, B:E.47, B:E.60 MN.8: 5 residues within 4Å: Chain C: H.106, D.108, H.162, R.188 Ligands: AKG.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.106, C:D.108, C:H.162 MN.10: 3 residues within 4Å: Chain A: H.50 Chain C: E.47, E.60 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:E.47, C:E.47, C:E.60, A:H.50

3 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 14 residues within 4Å: Chain A: I.55, H.93, L.95, I.103, H.106, D.108, M.128, Y.150, H.162, R.182, S.184, I.186, R.188 Ligands: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.103, A:I.186 Hydrogen bonds: A:Y.150, A:S.184 Salt bridges: A:H.93, A:H.106, A:R.182, A:R.188 AKG.6: 13 residues within 4Å: Chain B: I.55, H.93, L.95, I.103, H.106, D.108, M.128, Y.150, H.162, R.182, S.184, R.188 Ligands: MN.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.95, B:I.103 Hydrogen bonds: B:Y.150, B:Y.150, B:S.184 Salt bridges: B:H.93, B:H.106, B:R.182, B:R.188 AKG.9: 14 residues within 4Å: Chain C: I.55, H.93, L.95, I.103, H.106, D.108, M.128, Y.150, H.162, R.182, S.184, I.186, R.188 Ligands: MN.8 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.103, C:I.186 Hydrogen bonds: C:Y.150, C:Y.150, C:S.184 Salt bridges: C:H.93, C:H.106, C:R.182, C:R.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, G. et al., The atomic resolution structure of human AlkB homolog 7 (ALKBH7), a key protein for programmed necrosis and fat metabolism. J.Biol.Chem. (2014)

Release Date

2014-08-20

Peptides

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial

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