SMTL ID : 4oct.1 (1 other biounit)

Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.132, D.134, H.194 Ligands: AKG.2, UNX.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.132, A:D.134, A:H.194

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

AKG.2: 15 residues within 4Å: Chain A: N.121, Y.123, I.129, H.132, D.134, L.154, H.194, I.196, R.205, V.207, I.209, R.211 Ligands: MN.1, UNX.7, UNX.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.154 Hydrogen bonds: A:N.121 Salt bridges: A:K.60, A:H.132, A:R.205, A:R.211

9 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 3 residues within 4Å: Chain A: P.93, E.94, W.95 No protein-ligand interaction detected (PLIP) UNX.4: 4 residues within 4Å: Chain A: I.101, V.105, E.112, G.113 No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: V.52, D.53, R.54 No protein-ligand interaction detected (PLIP) UNX.6: 5 residues within 4Å: Chain A: H.50, F.62, G.66, Y.67, Y.84 No protein-ligand interaction detected (PLIP) UNX.7: 5 residues within 4Å: Chain A: K.60, Y.67, V.119, R.211 Ligands: AKG.2 No protein-ligand interaction detected (PLIP) UNX.8: 5 residues within 4Å: Chain A: S.117, A.118, V.119, I.209, R.211 No protein-ligand interaction detected (PLIP) UNX.9: 5 residues within 4Å: Chain A: F.114, E.140, P.142, R.211, K.212 No protein-ligand interaction detected (PLIP) UNX.10: 4 residues within 4Å: Chain A: V.39, N.59, Y.61, D.122 No protein-ligand interaction detected (PLIP) UNX.11: 5 residues within 4Å: Chain A: I.143, L.184, H.194 Ligands: MN.1, AKG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, C. et al., Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. J.Biol.Chem. (2014)

Release Date

2014-04-16

Peptides

RNA demethylase ALKBH5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA demethylase ALKBH5

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