SMTL ID : 3s57.1

ABH2 cross-linked with undamaged dsDNA-1 containing cofactors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.117, D.119, H.182 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.117, A:D.119, A:H.182, H2O.5

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

AKG.2: 12 residues within 4Å: Chain A: L.103, N.105, Y.107, I.114, H.117, D.119, L.164, H.182, R.194, N.196, R.200 Ligands: MN.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.105, A:N.105, A:Y.107, A:S.132, A:S.132 Water bridges: A:N.196, A:T.198, A:R.200, A:R.200 Salt bridges: A:H.117, A:R.194, A:R.200

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.53, V.54, R.56, K.57, K.108, D.112 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.57, A:K.108, A:K.108 Water bridges: A:R.106, A:D.112, A:D.112 GOL.4: 4 residues within 4Å: Chain A: R.4, H.5, I.6, R.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.4, A:R.7, A:R.7 Water bridges: A:V.159

1 x XL3: propane-1-thiol(Non-covalent)

XL3.5: 6 residues within 4Å: Chain A: H.113, C.115 Chain B: A.9, C.10 Chain C: A.5, G.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yi, C. et al., Duplex interrogation by a direct DNA repair protein in search of base damage. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-06-06

Peptides

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2

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