SMTL ID : 9bbg.1

Co-crystal structure of human DDB1 bound to fragment UB028671

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.467, A:Q.468 Water bridges: A:V.465, A:Q.469 Salt bridges: A:R.416

1 x 01: 1H-indol-6-amine

01.3: 7 residues within 4Å: Chain A: P.71, E.74, L.78, I.90, R.105, L.147, D.148 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.71, A:P.71, A:L.78, A:R.105 Hydrogen bonds: A:L.147

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

EDO.4: 7 residues within 4Å: Chain A: N.18, G.19, A.36, I.63, A.64, V.65, M.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.63, A:M.66 Water bridges: A:M.66, A:M.66 EDO.5: 6 residues within 4Å: Chain A: I.1064, K.1065, S.1066, K.1069, I.1070, E.1071 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.1064, A:S.1066, A:E.1071 EDO.6: 7 residues within 4Å: Chain A: Q.729, V.731, S.732, N.828, T.829, Q.854, Y.855 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.732, A:N.828, A:T.829 Water bridges: A:Y.855 EDO.7: 3 residues within 4Å: Chain A: N.674, L.675, K.676 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.674 EDO.8: 6 residues within 4Å: Chain A: E.877, F.878, N.879, T.918, K.919, G.920 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.877, A:N.879, A:T.918, A:G.920 Water bridges: A:G.880, A:G.920 EDO.9: 4 residues within 4Å: Chain A: G.331, D.332, E.386, R.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.332, A:D.332, A:E.386 Water bridges: A:L.719

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

UNX.10: 4 residues within 4Å: Chain A: V.17, K.37, S.333, F.355 No protein-ligand interaction detected (PLIP) UNX.11: 3 residues within 4Å: Chain A: L.488, V.489, S.490 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 UB028671. 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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