MolNFT v1 · #128746 · protein
Crystal structure of DNA cross-link repair protein 1A in complex with cefotaxime
5NZY · DNA cross-link repair 1A protein: “Crystal structure of DNA cross-link repair protein 1A in complex with cefotaxime”. X-ray diffraction, 2 ligands (CE3, NI), 3 pockets (best druggability 0.57). MolNFT v1 #128746 on GenesisL1: 3D…
- PDB
- 5NZY
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA cross-link repair 1A protein
- UniProt
- Q6PJP8
- Ligands
- CE3, NI
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA cross-link repair 1A protein | protein | 341 | 33% helix, 23% strand | Q6PJP8 |
Ligands and binding sites
- CE3 · (6R,7R)-3-(acetyloxymethyl)-7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid · ligand · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.57 | 0.80 | 39 | empty |
| 2 | 107 | 0.35 | 0.73 | 19 | empty |
| 3 | 78 | 0.34 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NZY · Crystal structure of DNA cross-link repair protein 1A in complex with Cefotaxime · the same entry in another collection · chain A against A, TM-score 1.00
- Q6PJP8 · AlphaFold monomer V2.0 prediction for DNA cross-link repair 1A protein (Q6PJP8) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6PJP8
- Elsewhere: RCSB PDB 5NZY · PDBe 5NZY · UniProt Q6PJP8
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