Research workbench
Mycobacterium smegmatis ATP synthase B-delta state 1
Analyse Mycobacterium smegmatis ATP synthase B-delta state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NKD
- Type
- protein
- Length
- 643 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase subunit B-delta; ATP…
- EC
- 7.1.2.2
- UniProt
- A0R202, A0R200, A0R203, A0R204
- Pockets
- 7 · best druggability 0.69
Structure
electron microscopy · 8 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 94 | 14% helix, 26% strand | A0R202 |
| B | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 47 | 23% helix, 17% strand | A0R202 |
| C | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 32 | 47% helix, 0% strand | A0R202 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 39 | 0% helix, 36% strand | A0R200 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 41 | 0% helix, 44% strand | A0R200 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 17 | 0% helix, 12% strand | A0R200 |
| d | ATP synthase subunit B-delta | protein | 336 | 68% helix, 6% strand | A0R203 |
| b | ATP synthase subunit B | protein | 37 | 73% helix, 0% strand | A0R204 |
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 | 552 | 0.69 | 0.79 | 70 | empty |
| 2 | 560 | 0.62 | 0.75 | 51 | empty |
| 3 | 277 | 0.57 | 0.78 | 37 | empty |
| 4 | 396 | 0.57 | 0.74 | 40 | empty |
| 5 | 52 | 0.34 | 0.78 | 17 | empty |
Interfaces
12 interfaces between chains.
- A–d · 1174 Ų buried · 20 hydrogen bonds · protein-protein
- d–b · 869 Ų buried · 3 hydrogen bonds · protein-protein
- B–d · 704 Ų buried · 4 hydrogen bonds · protein-protein
- C–d · 671 Ų buried · 5 hydrogen bonds · protein-protein
- A–b · 493 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7NKD · Mycobacterium smegmatis ATP synthase b-delta state 1 · the same entry in another collection · chain b against b, TM-score 1.00
- A0R200 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta (A0R200) · a predicted model of the same protein · chain E against A, TM-score 0.94
- A0R203 · AlphaFold monomer V2.0 prediction for ATP synthase subunit B-delta (A0R203) · a predicted model of the same protein · chain d against A, TM-score 0.92
- A0R202 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha (A0R202) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 A0R202
- Every structure of UniProt A0R200
- Every structure of UniProt A0R203
- Every structure of UniProt A0R204
- Elsewhere: RCSB PDB 7NKD · PDBe 7NKD · UniProt A0R202 · UniProt A0R200 · UniProt A0R203 · UniProt A0R204
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