SMTL ID : 2iuw.1

Crystal structure of human ABH3 in complex with iron ion and 2- oxoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: H.143, D.145, H.209 Ligands: AKG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.143, A:D.145, A:H.209, H2O.6 FE.2: 2 residues within 4Å: Chain A: R.26, E.27 No protein-ligand interaction detected (PLIP) FE.3: 7 residues within 4Å: Chain A: S.33, L.34, S.35, G.38, S.40, A.202, D.206 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.33, A:G.38, A:S.40, A:D.206 FE.9: 4 residues within 4Å: Chain B: H.143, D.145, H.209 Ligands: AKG.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.143, B:D.145, B:H.209, H2O.15 FE.10: 2 residues within 4Å: Chain B: R.26, E.27 No protein-ligand interaction detected (PLIP) FE.11: 7 residues within 4Å: Chain B: S.33, L.34, S.35, G.38, S.40, A.202, D.206 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.33, B:G.38, B:S.40, B:D.206

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

AKG.4: 13 residues within 4Å: Chain A: L.129, N.131, Y.133, H.143, D.145, F.167, L.191, H.209, V.211, R.221, N.223, R.227 Ligands: FE.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.167, A:V.211 Hydrogen bonds: A:N.131, A:T.225 Water bridges: A:S.158, A:N.223, A:R.227, A:R.227, A:R.227, A:R.227 Salt bridges: A:H.143, A:R.221, A:R.227 AKG.12: 13 residues within 4Å: Chain B: L.129, N.131, Y.133, H.143, D.145, F.167, L.191, H.209, V.211, R.221, N.223, R.227 Ligands: FE.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.167, B:V.211 Hydrogen bonds: B:N.131, B:T.225 Water bridges: B:S.158, B:N.223, B:R.227, B:R.227, B:R.227, B:R.227 Salt bridges: B:H.143, B:R.221, B:R.227

8 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 5 residues within 4Å: Chain A: R.41, C.43, Y.45, I.198, E.200 No protein-ligand interaction detected (PLIP) BME.6: 7 residues within 4Å: Chain A: T.37, C.153, G.201, A.202 Chain B: E.118, E.119, G.122 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.118, B:E.119 BME.7: 2 residues within 4Å: Chain A: C.62, P.220 No protein-ligand interaction detected (PLIP) BME.8: 6 residues within 4Å: Chain A: S.139, V.140, D.141, R.210, P.212, K.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.141, A:D.141, A:R.210 BME.13: 5 residues within 4Å: Chain B: R.41, C.43, Y.45, I.198, E.200 No protein-ligand interaction detected (PLIP) BME.14: 7 residues within 4Å: Chain A: E.118, E.119, G.122 Chain B: T.37, C.153, G.201, A.202 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.118, A:E.119 BME.15: 2 residues within 4Å: Chain B: C.62, P.220 No protein-ligand interaction detected (PLIP) BME.16: 6 residues within 4Å: Chain B: S.139, V.140, D.141, R.210, P.212, K.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.141, B:D.141, B:R.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sundheim, O. et al., Human Abh3 Structure and Key Residues for Oxidative Demethylation to Reverse DNA/RNA Damage. Embo J. (2006)

Release Date

2006-07-26

Peptides

ALKYLATED REPAIR PROTEIN ALKB HOMOLOG 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ALKYLATED REPAIR PROTEIN ALKB HOMOLOG 3