MolNFT v1 · #121896 · protein
Crystal structure of the RV1700 (mt adprase) E142Q mutant
5I8U · ADP-ribose pyrophosphatase: “Crystal structure of the RV1700 (mt adprase) E142Q mutant”. X-ray diffraction, 2 ligands (NA, SO4), 14 pockets (best druggability 0.79). MolNFT v1 #121896 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5I8U
- Type
- protein
- Length
- 1,378 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribose pyrophosphatase
- EC
- 3.6.1.13
- UniProt
- A0A045KHE5
- Ligands
- NA, SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 197 | 21% helix, 43% strand | A0A045KHE5 |
| A | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 198 | 20% helix, 41% strand | A0A045KHE5 |
| B | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 202 | 21% helix, 39% strand | A0A045KHE5 |
| C | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 203 | 22% helix, 42% strand | A0A045KHE5 |
| D | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 192 | 21% helix, 43% strand | A0A045KHE5 |
| E | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 190 | 22% helix, 44% strand | A0A045KHE5 |
| F | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 196 | 23% helix, 44% strand | A0A045KHE5 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains C
- SO4 · Sulfate ion · ion · 3 copies · chains G, A, B, C, D
- FMT · Formic acid · additive · 2 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.79 | 0.80 | 127 | FMT, NA |
| 2 | 419 | 0.66 | 0.79 | 51 | empty |
| 3 | 560 | 0.64 | 0.75 | 60 | PEG |
| 4 | 382 | 0.62 | 0.77 | 46 | empty |
| 5 | 260 | 0.62 | 0.80 | 35 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2728 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2688 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2657 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 643 Ų buried · 7 hydrogen bonds · protein-protein
- G–F · 631 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5I8U · Crystal Structure of the RV1700 (MT ADPRASE) E142Q mutant · the same entry in another collection · chain G against G, 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 A0A045KHE5
- Elsewhere: RCSB PDB 5I8U · PDBe 5I8U · UniProt A0A045KHE5
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