SMTL ID : 6oe7.1

Crystal structure of HMCES cross-linked to DNA abasic site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x DG- DT- DC- DT- DG- DG: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')(Non-covalent)

DG-DT-DC-DT-DG-DG.1: 9 residues within 4Å: Chain A: W.80, K.82, R.105 Chain B: C.1, C.2, A.3, G.4, A.5, C.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.91 Hydrogen bonds: A:N.92, A:N.92, A:T.100, A:T.100, A:K.104, A:R.105, A:S.106 Salt bridges: A:K.104, A:K.104 pi-Stacking: A:W.80 DG-DT-DC-DT-DG-DG.11: 14 residues within 4Å: Chain A: R.3, S.44, P.45, Q.46, Q.90, S.258, R.259 Chain C: C.1, C.2, A.3, G.4, A.5, C.6 Ligands: EDO.8 Protein-ligand interaction information (PLIP) not available

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

UNX.2: 2 residues within 4Å: Chain A: T.14 Ligands: UNX.9 No protein-ligand interaction detected (PLIP) UNX.6: 3 residues within 4Å: Chain A: R.32, D.33 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) UNX.9: 2 residues within 4Å: Chain A: R.15 Ligands: UNX.2 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: F.91 Chain B: A.5, C.6 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain C: A.5, C.6 No protein-ligand interaction detected (PLIP)

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: A.16, C.17, L.52, R.67, L.172, T.174, E.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.67 Water bridges: A:C.17, A:R.67 EDO.4: 5 residues within 4Å: Chain A: K.36, N.48, V.190, L.191, Y.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.36, A:Y.192, A:Y.192 EDO.5: 4 residues within 4Å: Chain A: D.33, P.34, D.35 Ligands: UNX.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.33, A:D.35, A:D.35 EDO.7: 2 residues within 4Å: Chain A: T.247, F.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.247, A:T.247 EDO.8: 3 residues within 4Å: Chain A: Q.46 Ligands: DG-DT-DC-DT-DG-DG.11, DG-DT-DC-DT-DG-DG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.46, A:L.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halabelian, L. et al., Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-04-24

Peptides

Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein

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