SMTL ID : 6oeb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x DC- DC- DA- DG- DA- DC- DG- DT- DT: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3')(Non-covalent)

DC-DC-DA-DG-DA-DC-DG-DT-DT.1: 22 residues within 4Å: Chain A: W.80, Q.90, F.91, N.92, N.95, C.96, R.97, K.104, R.105, S.106, F.107, T.198, H.209, R.211 Ligands: DG-DT-DC-DT-DG-DG.2, DG-DT-DC-DT-DG-DG.2, DG-DT-DC-DT-DG-DG.2, DG-DT-DC-DT-DG-DG.2, DG-DT-DC-DT-DG-DG.2, DG-DT-DC-DT-DG-DG.2, UNX.18, DC-DC-DA-DG-DA-DC-DG-DT-DT.20 Protein-ligand interaction information (PLIP) not available DC-DC-DA-DG-DA-DC-DG-DT-DT.20: 15 residues within 4Å: Chain A: G.2, R.3, P.45, W.127, R.136, N.256, N.257 Ligands: DC-DC-DA-DG-DA-DC-DG-DT-DT.1, DG-DT-DC-DT-DG-DG.21, DG-DT-DC-DT-DG-DG.21, DG-DT-DC-DT-DG-DG.21, DG-DT-DC-DT-DG-DG.21, DG-DT-DC-DT-DG-DG.21, DG-DT-DC-DT-DG-DG.21, UNX.22 Protein-ligand interaction information (PLIP) not available

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.2: 11 residues within 4Å: Chain A: W.80, K.82, R.105, K.108 Ligands: DC-DC-DA-DG-DA-DC-DG-DT-DT.1, DC-DC-DA-DG-DA-DC-DG-DT-DT.1, DC-DC-DA-DG-DA-DC-DG-DT-DT.1, DC-DC-DA-DG-DA-DC-DG-DT-DT.1, DC-DC-DA-DG-DA-DC-DG-DT-DT.1, DC-DC-DA-DG-DA-DC-DG-DT-DT.1, EDO.19 Protein-ligand interaction information (PLIP) not available DG-DT-DC-DT-DG-DG.21: 14 residues within 4Å: Chain A: R.3, S.44, P.45, Q.46, Q.90, S.258, R.259 Ligands: DC-DC-DA-DG-DA-DC-DG-DT-DT.20, DC-DC-DA-DG-DA-DC-DG-DT-DT.20, DC-DC-DA-DG-DA-DC-DG-DT-DT.20, DC-DC-DA-DG-DA-DC-DG-DT-DT.20, DC-DC-DA-DG-DA-DC-DG-DT-DT.20, DC-DC-DA-DG-DA-DC-DG-DT-DT.20, EDO.23 Protein-ligand interaction information (PLIP) not available

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

EDO.3: 7 residues within 4Å: Chain A: K.36, N.48, P.71, V.190, L.191, Y.192 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.48, A:Y.192, A:Y.192 EDO.4: 7 residues within 4Å: Chain A: R.32, D.33, F.58, A.70, P.71, Y.192 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.71 EDO.5: 8 residues within 4Å: Chain A: A.16, C.17, A.18, L.52, R.67, L.172, T.174, E.219 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.17, A:R.67 Water bridges: A:A.16, A:L.172, A:L.172, A:T.174 EDO.6: 5 residues within 4Å: Chain A: H.7, P.39, S.40, Y.41, N.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.261, A:N.261 EDO.7: 3 residues within 4Å: Chain A: D.33, P.34, D.35 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.33, A:D.33, A:D.35, A:D.35 EDO.19: 2 residues within 4Å: Ligands: DG-DT-DC-DT-DG-DG.2, DG-DT-DC-DT-DG-DG.2 No protein-ligand interaction detected (PLIP) EDO.23: 4 residues within 4Å: Chain A: Q.46, N.92 Ligands: DG-DT-DC-DT-DG-DG.21, DG-DT-DC-DT-DG-DG.21 No protein-ligand interaction detected (PLIP)

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

UNX.8: 1 residues within 4Å: Chain A: F.228 No protein-ligand interaction detected (PLIP) UNX.9: 1 residues within 4Å: Chain A: G.229 No protein-ligand interaction detected (PLIP) UNX.10: 1 residues within 4Å: Chain A: K.113 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: R.15 Ligands: UNX.12 No protein-ligand interaction detected (PLIP) UNX.12: 1 residues within 4Å: Ligands: UNX.11 No protein-ligand interaction detected (PLIP) UNX.13: 1 residues within 4Å: Chain A: I.208 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: R.23, Q.25 No protein-ligand interaction detected (PLIP) UNX.15: 1 residues within 4Å: Chain A: P.160 No protein-ligand interaction detected (PLIP) UNX.16: 4 residues within 4Å: Chain A: T.14, P.29, W.31 Ligands: UNX.17 No protein-ligand interaction detected (PLIP) UNX.17: 3 residues within 4Å: Chain A: E.30, W.31 Ligands: UNX.16 No protein-ligand interaction detected (PLIP) UNX.18: 3 residues within 4Å: Chain A: F.91 Ligands: DC-DC-DA-DG-DA-DC-DG-DT-DT.1, DC-DC-DA-DG-DA-DC-DG-DT-DT.1 No protein-ligand interaction detected (PLIP) UNX.22: 2 residues within 4Å: Ligands: DC-DC-DA-DG-DA-DC-DG-DT-DT.20, DC-DC-DA-DG-DA-DC-DG-DT-DT.20 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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