MolNFT v1 · #170421 · protein
The crystal structure of human MACROD2 in space group P43
6Y73 · ADP-ribose glycohydrolase MACROD2: “The crystal structure of human MACROD2 in space group P43”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #170421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Y73
- Type
- protein
- Length
- 1,729 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribose glycohydrolase MACROD2
- EC
- 3.5.1.-, 3.2.2.-
- UniProt
- A1Z1Q3
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 216 | 50% helix, 16% strand | A1Z1Q3 |
| B, C, F, G | ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 215 | 50% helix, 17% strand | A1Z1Q3 |
| D | ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 218 | 49% helix, 17% strand | A1Z1Q3 |
| E | ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 218 | 50% helix, 16% strand | A1Z1Q3 |
| H | ADP-ribose glycohydrolase MACROD2 (EC 3.5.1.-, 3.2.2.-) | protein | 217 | 49% helix, 16% strand | A1Z1Q3 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, C, B, D, G
- TLA · L(+)-tartaric acid · additive · 5 copies · chains B, C, F, D, G, H
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.79 | 0.80 | 104 | GOL |
| 2 | 1043 | 0.78 | 0.80 | 96 | empty |
| 3 | 724 | 0.75 | 0.80 | 76 | DMS |
| 4 | 575 | 0.71 | 0.79 | 36 | empty |
| 5 | 350 | 0.63 | 0.79 | 37 | empty |
Interfaces
10 interfaces between chains.
- E–F · 646 Ų buried · 6 hydrogen bonds · protein-protein
- E–H · 646 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 639 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 509 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 389 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6Y73 · The crystal structure of human MACROD2 in space group P43 · the same entry in another collection · chain H against H, TM-score 1.00
- A1Z1Q3 · AlphaFold monomer V2.0 prediction for ADP-ribose glycohydrolase MACROD2 (A1Z1Q3) · a predicted model of the same protein · chain B 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 A1Z1Q3
- Elsewhere: RCSB PDB 6Y73 · PDBe 6Y73 · UniProt A1Z1Q3
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