MolNFT v1 · #60562 · protein
Crystal structure of a periplasmic putative metal binding protein
3CVG: “Crystal structure of a periplasmic putative metal binding protein”. X-ray diffraction, 1 ligand (CA), 15 pockets (best druggability 0.80). MolNFT v1 #60562 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CVG
- Type
- protein
- Length
- 1,015 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative metal binding protein
- UniProt
- Q1DXA6
- Ligands
- CA
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative metal binding protein | protein | 270 | 37% helix, 24% strand | Q1DXA6 |
| C | Putative metal binding protein | protein | 207 | 33% helix, 23% strand | Q1DXA6 |
| D | Putative metal binding protein | protein | 268 | 37% helix, 23% strand | Q1DXA6 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.80 | 0.95 | 28 | empty |
| 2 | 539 | 0.73 | 0.82 | 68 | CA |
| 3 | 584 | 0.72 | 0.80 | 67 | CA |
| 4 | 95 | 0.58 | 0.86 | 18 | empty |
| 5 | 260 | 0.51 | 0.75 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1386 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1255 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 601 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 114 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3CVG · Crystal structure of a periplasmic putative metal binding protein · 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 Q1DXA6
- Elsewhere: RCSB PDB 3CVG · PDBe 3CVG · UniProt Q1DXA6
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