SMTL ID : 1wyw.1

Crystal Structure of SUMO1-conjugated thymine DNA glycosylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: G.122, K.123, F.143, P.161, S.162 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: P.44, G.45, W.51, N.65, H.66 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: E.9, L.10, L.11 Ligand excluded by PLIP

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 7 residues within 4Å: Chain A: Q.174, D.175, K.176, V.177, H.178, Y.204 Chain B: R.54 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.174, H2O.1 MG.5: 5 residues within 4Å: Chain A: I.27, G.29, Y.43, T.81, N.82 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.27, A:Y.43, A:T.81, H2O.1 MG.7: 1 residues within 4Å: Chain B: H.43 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.43, H2O.6, H2O.6, H2O.7, H2O.7 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: T.41, T.76, K.78 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.76

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain B: K.48, A.72, D.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.48, B:D.73, B:D.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baba, D. et al., Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Nature (2005)

Release Date

2005-06-21

Peptides

G/T mismatch-specific thymine DNA glycosylase: A
Ubiquitin-like protein SMT3C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

G/T mismatch-specific thymine DNA glycosylase

Ubiquitin-like protein SMT3C

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