Research workbench
Crystal structure of the calcium chelating immunodominant antigen, calcium dodecin (RV0379),FROM mycobacterium tuberculosis with a novel calcium-binding site
Analyse Crystal structure of the calcium chelating immunodominant antigen, calcium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ONR
- Type
- protein
- Length
- 838 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SECE2
- UniProt
- Q6MX43
- Ligands
- CA, PT
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, H, I, L | Protein transport protein SECE2 | protein | 71 | 21% helix, 48% strand | Q6MX43 |
| B, C, E | Protein transport protein SECE2 | protein | 70 | 21% helix, 49% strand | Q6MX43 |
| D, K | Protein transport protein SECE2 | protein | 67 | 19% helix, 51% strand | Q6MX43 |
| J | Protein transport protein SECE2 | protein | 68 | 22% helix, 50% strand | Q6MX43 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PT · Platinum (II) ion · metal · 3 copies · chains E, F, H, I
- FMT · Formic acid · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.72 | 0.83 | 42 | FMT |
| 2 | 461 | 0.72 | 0.82 | 40 | FMT |
| 3 | 466 | 0.72 | 0.82 | 46 | FMT |
| 4 | 478 | 0.71 | 0.81 | 45 | FMT |
| 5 | 418 | 0.71 | 0.82 | 45 | FMT |
Interfaces
30 interfaces between chains.
- E–I · 683 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 673 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 639 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 638 Ų buried · 7 hydrogen bonds · protein-protein
- C–H · 636 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3ONR · Crystal structure of the calcium chelating immunodominant antigen, calcium dodecin… · the same entry in another collection · chain L against L, 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 Q6MX43
- Elsewhere: RCSB PDB 3ONR · PDBe 3ONR · UniProt Q6MX43
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