MolNFT v1 · #157042 · protein
Carbon regulatory pii-like protein sbtb from cyanobium sp. 7001 bound to AMP
6MMO: “Carbon regulatory pii-like protein sbtb from cyanobium sp. 7001 bound to AMP”. X-ray diffraction, 3 ligands (AMP, MG, CL), 8 pockets (best druggability 0.71). MolNFT v1 #157042 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6MMO
- Type
- protein
- Length
- 524 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon regulatory pii-like protein sbtb
- UniProt
- B5II98
- Ligands
- AMP, MG, CL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbon regulatory pii-like protein sbtb | protein | 91 | 31% helix, 44% strand | B5II98 |
| B | Carbon regulatory pii-like protein sbtb | protein | 84 | 33% helix, 43% strand | B5II98 |
| C | Carbon regulatory pii-like protein sbtb | protein | 87 | 32% helix, 45% strand | B5II98 |
| D | Carbon regulatory pii-like protein sbtb | protein | 86 | 33% helix, 44% strand | B5II98 |
| E | Carbon regulatory pii-like protein sbtb | protein | 89 | 31% helix, 45% strand | B5II98 |
| F | Carbon regulatory pii-like protein sbtb | protein | 87 | 32% helix, 44% strand | B5II98 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 6 copies · chains A, B, C, E, D, F
- MG · Magnesium ion · metal · 7 copies · chains A, B, D, C, E, F
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.71 | 0.77 | 71 | MG |
| 2 | 347 | 0.64 | 0.79 | 42 | AMP |
| 3 | 280 | 0.61 | 0.80 | 35 | AMP |
| 4 | 91 | 0.60 | 0.88 | 24 | empty |
| 5 | 262 | 0.58 | 0.78 | 31 | AMP, MG |
Interfaces
9 interfaces between chains.
- A–B · 860 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 773 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 767 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 750 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 692 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6MMO · Carbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 bound to AMP · 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 B5II98
- Elsewhere: RCSB PDB 6MMO · PDBe 6MMO · UniProt B5II98
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