SMTL ID : 9bbh.1

Co-crystal structure of human DDB1 bound to fragment UB028670

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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.264, A:R.265 Water bridges: A:A.223, A:A.223, A:H.263, A:H.263 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 Water bridges: A:N.464, A:N.464, A:V.465 Salt bridges: A:R.416

2 x VVP: 4-methoxy-1H-indole(Non-covalent)

VVP.3: 8 residues within 4Å: Chain A: T.15, V.17, K.37, Y.44, F.325, S.333, F.355, T.356 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.17, A:F.325, A:F.355, A:F.355 Hydrogen bonds: A:K.37, A:T.356 Water bridges: A:T.356 pi-Cation interactions: A:K.37 VVP.4: 11 residues within 4Å: Chain A: P.71, E.74, I.90, R.105, A.106, P.146, L.147, D.148, R.149, N.151, L.154 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.71, A:I.90, A:A.106 Hydrogen bonds: A:E.74, A:E.74, A:D.148

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

EDO.5: 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.6: 6 residues within 4Å: Chain A: Q.729, S.732, N.828, T.829, Q.854, Y.855 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.828, A:T.829, A:Y.855 Water bridges: A:Y.855

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

UNX.7: 2 residues within 4Å: Chain A: K.62, N.1036 No protein-ligand interaction detected (PLIP) UNX.8: 1 residues within 4Å: Chain A: S.1066 No protein-ligand interaction detected (PLIP) UNX.9: 4 residues within 4Å: Chain A: F.878, T.918, K.919, G.920 No protein-ligand interaction detected (PLIP) UNX.10: 4 residues within 4Å: Chain A: S.504, D.544, I.545, T.546 No protein-ligand interaction detected (PLIP) UNX.11: 1 residues within 4Å: Chain A: L.338 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 UB028670. 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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