MolNFT v1 · #182098 · protein
Chryseobacterium gregarium ripp-associated ATP-grasp ligase in complex with ADP, and a leader and core peptide
7MGV · Cdnc: “Chryseobacterium gregarium ripp-associated ATP-grasp ligase in complex with ADP, and a leader and core peptide”. X-ray diffraction, 1 ligand (ADP), 7 pockets (best druggability 0.81). MolNFT v1 #182098 on GenesisL1: 3D…
- PDB
- 7MGV
- Type
- protein
- Length
- 701 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdnc; CDNA3 leader peptide; CDNA3 core peptide
- Ligands
- ADP
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cdnc | protein | 333 | 36% helix, 29% strand | — |
| V, U | CDNA3 leader peptide | protein | 12 | 42% helix, 25% strand | — |
| T | CDNA3 core peptide | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B, T
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.81 | 0.83 | 86 | ADP |
| 2 | 487 | 0.72 | 0.81 | 54 | empty |
| 3 | 71 | 0.48 | 0.83 | 18 | empty |
| 4 | 169 | 0.47 | 0.76 | 25 | ADP |
| 5 | 51 | 0.47 | 0.86 | 19 | GOL |
Interfaces
8 interfaces between chains.
- A–B · 3426 Ų buried · 54 hydrogen bonds · protein-protein
- A–U · 809 Ų buried · 6 hydrogen bonds · protein-protein
- B–T · 796 Ų buried · 20 hydrogen bonds · protein-protein
- V–B · 751 Ų buried · 6 hydrogen bonds · protein-protein
- U–B · 287 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7MGV · Chryseobacterium gregarium RiPP-associated ATP-grasp ligase in complex with ADP, and a… · 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
- Elsewhere: RCSB PDB 7MGV · PDBe 7MGV
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