MolNFT v1 · #138771 · protein
Crystal structure of the C-terminal domain of outer membrane protein a (ompa) from capnocytophaga gingivalis
5WTP · Ompa family protein: “Crystal structure of the C-terminal domain of outer membrane protein a (ompa) from capnocytophaga gingivalis”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.48). MolNFT v1 #138771 on…
- PDB
- 5WTP
- Type
- protein
- Length
- 367 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ompa family protein
- UniProt
- C2M2E7
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ompa family protein | protein | 124 | 44% helix, 15% strand | C2M2E7 |
| B | Ompa family protein | protein | 121 | 46% helix, 16% strand | C2M2E7 |
| C | Ompa family protein | protein | 122 | 48% helix, 17% strand | C2M2E7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 29 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.48 | 0.76 | 31 | SO4 |
| 2 | 110 | 0.44 | 0.78 | 23 | SO4 |
| 3 | 115 | 0.42 | 0.77 | 22 | SO4 |
| 4 | 62 | 0.42 | 0.81 | 23 | empty |
| 5 | 91 | 0.32 | 0.73 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 612 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WTP · Crystal structure of the C-terminal domain of outer membrane protein A (OmpA) from… · 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 C2M2E7
- Elsewhere: RCSB PDB 5WTP · PDBe 5WTP · UniProt C2M2E7
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