Research workbench
Structure of mycobacterium tuberculosis adenylyl cyclase RV1625C / cya
Analyse Structure of mycobacterium tuberculosis adenylyl cyclase RV1625C / cya in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YZK
- Type
- protein
- Length
- 990 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate cyclase; Nanobody NB4
- EC
- 4.6.1.1
- UniProt
- A0A5R1ZCG6
- Ligands
- ONM, MN
- Pockets
- 13 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate cyclase (EC 4.6.1.1) | protein | 378 | 61% helix, 14% strand | A0A5R1ZCG6 |
| C, D | Nanobody NB4 | protein | 117 | 13% helix, 47% strand | — |
Ligands and binding sites
- ONM · 3'-O-(N-methylanthraniloyl)-guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.84 | 0.89 | 61 | empty |
| 2 | 582 | 0.83 | 0.88 | 59 | empty |
| 3 | 859 | 0.80 | 0.82 | 85 | empty |
| 4 | 883 | 0.72 | 0.76 | 71 | ONM, MN |
| 5 | 79 | 0.71 | 0.95 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4021 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 707 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 703 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7YZK · Structure of Mycobacterium tuberculosis adenylyl cyclase Rv1625c / Cya · 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 A0A5R1ZCG6
- Elsewhere: RCSB PDB 7YZK · PDBe 7YZK · UniProt A0A5R1ZCG6
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