SMTL ID : 9bbi.1

Co-crystal structure of human DDB1 bound to fragment UB028669

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.264, A:R.265 Water bridges: A:A.223, 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: 3-([1,3]oxazolo[4,5-b]pyridin-2-yl)aniline

01.3: 8 residues within 4Å: Chain A: I.35, K.37, E.42, Y.44, L.51, P.53, F.325, F.355 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.35, A:Y.44, A:P.53, A:F.325 Hydrogen bonds: A:K.37, A:Y.44 pi-Stacking: A:F.355, A:F.355

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

UNX.4: 1 residues within 4Å: Chain A: Y.318 No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: N.828, T.829, Q.854 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: A.64, M.66 No protein-ligand interaction detected (PLIP) UNX.7: 1 residues within 4Å: Chain A: S.1066 No protein-ligand interaction detected (PLIP) UNX.8: 2 residues within 4Å: Chain A: S.504, C.505 No protein-ligand interaction detected (PLIP) UNX.9: 2 residues within 4Å: Chain A: E.386, R.390 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 UB028669. 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

Related Entries With Identical Sequence