Research workbench
Crystal structure of nucleoside-triphosphatase / DITP/XTP pyrophosphatase from mycobacterium abscessus atcc 19977 / dsm 44196
Analyse Crystal structure of nucleoside-triphosphatase / DITP/XTP pyrophosphatase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WWD
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DITP/XTP pyrophosphatase
- EC
- 3.6.1.66
- UniProt
- B1MLZ4
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DITP/XTP pyrophosphatase (EC 3.6.1.66) | protein | 196 | 42% helix, 23% strand | B1MLZ4 |
| B | DITP/XTP pyrophosphatase (EC 3.6.1.66) | protein | 190 | 39% helix, 24% strand | B1MLZ4 |
| C | DITP/XTP pyrophosphatase (EC 3.6.1.66) | protein | 191 | 39% helix, 24% strand | B1MLZ4 |
| D | DITP/XTP pyrophosphatase (EC 3.6.1.66) | protein | 199 | 35% helix, 23% strand | B1MLZ4 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.66 | 0.78 | 73 | empty |
| 2 | 633 | 0.66 | 0.76 | 70 | empty |
| 3 | 341 | 0.62 | 0.79 | 37 | empty |
| 4 | 465 | 0.61 | 0.76 | 58 | empty |
| 5 | 358 | 0.61 | 0.78 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2302 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2114 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 961 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 925 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6WWD · Crystal structure of Nucleoside-triphosphatase / dITP/XTP pyrophosphatase from… · the same entry in another collection · chain D against D, TM-score 1.00
- B1MLZ4 · AlphaFold monomer V2.0 prediction for DITP/XTP pyrophosphatase (B1MLZ4) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 B1MLZ4
- Elsewhere: RCSB PDB 6WWD · PDBe 6WWD · UniProt B1MLZ4
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