SMTL ID : 6oea.1

Crystal structure of HMCES SRAP domain in complex with longer 3' overhang DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: 11 residues within 4Å: Chain A: W.80, K.82, R.105, K.108 Chain B: C.1, C.2, A.3, G.4, A.5, C.6 Ligands: EDO.17 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.91 Hydrogen bonds: A:N.92, 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.18: 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.21 Protein-ligand interaction information (PLIP) not available

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

EDO.2: 9 residues within 4Å: Chain A: K.36, N.48, P.71, M.72, R.73, V.190, L.191, Y.192 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.48, A:Y.192 EDO.3: 3 residues within 4Å: Chain A: D.33, P.34, D.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.33, A:D.35, A:D.35 EDO.4: 7 residues within 4Å: Chain A: A.16, C.17, L.52, R.67, L.120, T.174, E.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.67 Water bridges: A:A.16, A:C.17, A:L.172 EDO.5: 6 residues within 4Å: Chain A: D.33, F.58, A.70, P.71, Y.192 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.71 EDO.17: 2 residues within 4Å: Ligands: DG-DT-DC-DT-DG-DG.1, DG-DT-DC-DT-DG-DG.1 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain A: Q.46, N.92 Ligands: DG-DT-DC-DT-DG-DG.18, DG-DT-DC-DT-DG-DG.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.46

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

UNX.6: 1 residues within 4Å: Chain A: F.228 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: F.228, G.229 No protein-ligand interaction detected (PLIP) UNX.8: 2 residues within 4Å: Chain A: R.15 Ligands: UNX.10 No protein-ligand interaction detected (PLIP) UNX.9: 1 residues within 4Å: Chain A: Y.139 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: T.14 Ligands: UNX.8, UNX.12 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain A: E.30, W.31 Ligands: UNX.12 No protein-ligand interaction detected (PLIP) UNX.12: 5 residues within 4Å: Chain A: T.14, P.29, W.31 Ligands: UNX.10, UNX.11 No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain A: H.7, P.39, Y.41 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain A: H.7, L.8, P.9, P.39 No protein-ligand interaction detected (PLIP) UNX.15: 3 residues within 4Å: Chain A: F.91 Chain B: A.5, C.6 No protein-ligand interaction detected (PLIP) UNX.16: 1 residues within 4Å: Chain B: G.10 No protein-ligand interaction detected (PLIP) UNX.19: 2 residues within 4Å: Chain C: A.5, C.6 No protein-ligand interaction detected (PLIP) UNX.20: 1 residues within 4Å: Chain C: G.10 No protein-ligand interaction detected (PLIP)

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

2019-04-10

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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