SMTL ID : 9bbe.1

Co-crystal structure of human DDB1 bound to fragment UB028668

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 5 residues within 4Å: Chain A: I.222, H.263, N.264, R.265, Y.273 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.264, A:R.265 Water bridges: A:A.223 Salt bridges: A:H.263, A:R.265 TLA.2: 6 residues within 4Å: Chain A: R.416, N.464, V.465, A.466, H.467, Q.468 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.467, A:Q.468, A:Q.469 Water bridges: A:N.464, A:V.465 Salt bridges: A:R.416

1 x 01: 5-(4-methoxyphenyl)-3-[(3S)-pyrrolidin-3-yl]-1,2,4-oxadiazole

01.3: 10 residues within 4Å: Chain A: E.74, L.78, I.90, E.92, R.105, L.147, D.148, R.149, N.151, L.154 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.78, A:R.149 Hydrogen bonds: A:E.92, A:R.105

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

UNX.4: 2 residues within 4Å: Chain A: T.829, Q.854 No protein-ligand interaction detected (PLIP) UNX.5: 1 residues within 4Å: Chain A: L.338 No protein-ligand interaction detected (PLIP) UNX.6: 3 residues within 4Å: Chain A: G.58, S.1066, V.1067 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: A.64, M.66 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., Co-crystal structure of human DDB1 bound to fragment UB028668. To be published

Release Date

2024-06-12

Peptides

DNA damage-binding protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA damage-binding protein 1

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