Research workbench
Crystal structure of RV0983 from mycobacterium tuberculosis- proteolytically active form
Analyse Crystal structure of RV0983 from mycobacterium tuberculosis- proteolytically… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z9I
- Type
- protein
- Length
- 835 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable serine protease pepd; Sveqv; Gatv
- EC
- 3.4.21.-
- UniProt
- O53896
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable serine protease pepd (EC 3.4.21.-) | protein | 284 | 18% helix, 43% strand | O53896 |
| B | Probable serine protease pepd (EC 3.4.21.-) | protein | 269 | 18% helix, 38% strand | O53896 |
| C | Probable serine protease pepd (EC 3.4.21.-) | protein | 260 | 18% helix, 38% strand | O53896 |
| D, E | Sveqv | protein | 4 | 0% helix, 50% strand | — |
| F | Sveqv | protein | 5 | 0% helix, 40% strand | — |
| G | Gatv | protein | 4 | 0% helix, 50% strand | — |
| H | Gatv | protein | 2 | 0% helix, 0% strand | — |
| I | Gatv | protein | 3 | 0% helix, 33% strand | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.74 | 0.82 | 55 | empty |
| 2 | 505 | 0.64 | 0.76 | 59 | empty |
| 3 | 467 | 0.62 | 0.76 | 55 | empty |
| 4 | 492 | 0.61 | 0.75 | 47 | empty |
| 5 | 83 | 0.40 | 0.78 | 20 | empty |
Interfaces
10 interfaces between chains.
- A–C · 797 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 761 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 699 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 479 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 462 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2Z9I · Crystal structure of RV0983 from Mycobacterium tuberculosis- Proteolytically active form · the same entry in another collection · chain I against I, TM-score 1.00
- O53896 · AlphaFold monomer V2.0 prediction for serine protease pepd (O53896) · a predicted model of the same protein · chain A 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 O53896
- Elsewhere: RCSB PDB 2Z9I · PDBe 2Z9I · UniProt O53896
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