MolNFT v1 · #170423 · protein
BIL2 domain from T.THERMOPHILA BUBL1 locus (C1A-N143A)
6Y75 · NAD(P)(+)--arginine ADP-ribosyltransferase: “BIL2 domain from T.THERMOPHILA BUBL1 locus (C1A-N143A)”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.71). MolNFT v1 #170423 on GenesisL1: 3D structure, binding sites…
- PDB
- 6Y75
- Type
- protein
- Length
- 606 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)(+)--arginine ADP-ribosyltransferase
- EC
- 2.4.2.31
- UniProt
- Q236S9
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NAD(P)(+)--arginine ADP-ribosyltransferase (EC 2.4.2.31) | protein | 153 | 2% helix, 56% strand | Q236S9 |
| B, D | NAD(P)(+)--arginine ADP-ribosyltransferase (EC 2.4.2.31) | protein | 150 | 2% helix, 57% strand | Q236S9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.71 | 0.79 | 69 | empty |
| 2 | 263 | 0.59 | 0.78 | 22 | empty |
| 3 | 238 | 0.56 | 0.78 | 20 | FMT |
| 4 | 184 | 0.54 | 0.79 | 24 | empty |
| 5 | 121 | 0.53 | 0.82 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 798 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 794 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 489 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6Y75 · BIL2 domain from T.thermophila BUBL1 locus (C1A-N143A) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q236S9
- Elsewhere: RCSB PDB 6Y75 · PDBe 6Y75 · UniProt Q236S9
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