Research workbench
The crystal structure of human MACROD2 in space group P43212
Analyse The crystal structure of human MACROD2 in space group P43212 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y4Z
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
- EC
- 3.5.1.-, 3.2.2.-
- UniProt
- P0AA25, A1Z1Q3
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin 1,ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 221 | 51% helix, 16% strand | P0AA25, A1Z1Q3 |
| B | Thioredoxin 1,ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 216 | 50% helix, 17% strand | P0AA25, A1Z1Q3 |
| C | Thioredoxin 1,ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 214 | 50% helix, 17% strand | P0AA25, A1Z1Q3 |
| D | Thioredoxin 1,ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 215 | 49% helix, 17% strand | P0AA25, A1Z1Q3 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.76 | 0.79 | 68 | TLA |
| 2 | 662 | 0.76 | 0.81 | 69 | empty |
| 3 | 692 | 0.74 | 0.80 | 74 | empty |
| 4 | 859 | 0.71 | 0.77 | 72 | empty |
| 5 | 58 | 0.53 | 0.88 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 652 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 639 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 568 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 314 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6Y4Z · The crystal structure of human MACROD2 in space group P43212 · the same entry in another collection · chain D against D, TM-score 1.00
- A1Z1Q3 · AlphaFold monomer V2.0 prediction for ADP-ribose glycohydrolase MACROD2 (A1Z1Q3) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P0AA25
- Every structure of UniProt A1Z1Q3
- Elsewhere: RCSB PDB 6Y4Z · PDBe 6Y4Z · UniProt P0AA25 · UniProt A1Z1Q3
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