Research workbench
Mycobacterium tuberculosis RV1957 secb-like chaperone in complex with a chad peptide from RV1956 HIGA1 antitoxin
Analyse Mycobacterium tuberculosis RV1957 secb-like chaperone in complex with a chad… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MTW
- Type
- protein
- Length
- 586 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secb-like chaperone RV1957; Antitoxin HIGA1
- UniProt
- P95257, P9WJA7
- Ligands
- CA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Secb-like chaperone RV1957 | protein | 138 | 26% helix, 42% strand | P95257 |
| D | Secb-like chaperone RV1957 | protein | 136 | 31% helix, 44% strand | P95257 |
| A | Secb-like chaperone RV1957 | protein | 138 | 31% helix, 40% strand | P95257 |
| B | Secb-like chaperone RV1957 | protein | 138 | 31% helix, 38% strand | P95257 |
| E, F, G | Antitoxin HIGA1 | protein | 12 | 0% helix, 8% strand | P9WJA7 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains D, A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains C, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.77 | 0.98 | 16 | DMS |
| 2 | 81 | 0.75 | 0.97 | 18 | DMS |
| 3 | 436 | 0.73 | 0.83 | 55 | empty |
| 4 | 309 | 0.62 | 0.79 | 37 | empty |
| 5 | 300 | 0.59 | 0.78 | 45 | empty |
Interfaces
16 interfaces between chains.
- C–A · 878 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 768 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 768 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 766 Ų buried · 3 hydrogen bonds · protein-protein
- C–G · 437 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5MTW · Mycobacterium tuberculosis Rv1957 SecB-like chaperone in complex with a ChAD peptide from… · the same entry in another collection · chain G against G, TM-score 1.00
- P95257 · AlphaFold monomer V2.0 prediction for secb-like chaperone RV1957 (P95257) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P9WJA7 · AlphaFold monomer V2.0 prediction for antitoxin HIGA1 (P9WJA7) · a predicted model of the same protein · chain E against A, TM-score 0.35
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 P95257
- Every structure of UniProt P9WJA7
- Elsewhere: RCSB PDB 5MTW · PDBe 5MTW · UniProt P95257 · UniProt P9WJA7
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