Research workbench
N-terminal RNase H domain of RV2228C from mycobacterium tuberculosis as a fusion protein with maltose binding protein
Analyse N-terminal RNase H domain of RV2228C from mycobacterium tuberculosis as a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HST
- Type
- protein
- Length
- 1,004 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein; Protein RV2228C/MT2287
- EC
- 3.-.-.-
- UniProt
- P0AEX9, P64955
- Ligands
- GLC
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein | protein | 365 | 46% helix, 19% strand | P0AEX9 |
| B | Protein RV2228C/MT2287 (EC 3.-.-.-) | protein | 139 | 42% helix, 32% strand | P64955 |
| C | Maltose-binding periplasmic protein | protein | 369 | 46% helix, 20% strand | P0AEX9 |
| D | Protein RV2228C/MT2287 (EC 3.-.-.-) | protein | 131 | 40% helix, 34% strand | P64955 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
- TAR · D(-)-tartaric acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.81 | 0.85 | 73 | GLC |
| 2 | 282 | 0.75 | 0.87 | 37 | GLC |
| 3 | 248 | 0.62 | 0.81 | 32 | empty |
| 4 | 274 | 0.51 | 0.74 | 39 | empty |
| 5 | 59 | 0.40 | 0.80 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 721 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 719 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 391 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HST · N-Terminal RNASE H domain of rv2228c from mycobacterium tuberculosis as a fusion protein… · the same entry in another collection · chain A against A, 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 P0AEX9
- Every structure of UniProt P64955
- Elsewhere: RCSB PDB 3HST · PDBe 3HST · UniProt P0AEX9 · UniProt P64955
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