MolNFT v1 · #138769 · protein
Crystal structure of the periplasmic portion of outer membrane protein a (ompa) from capnocytophaga gingivalis
5WTL · Ompa family protein: “Crystal structure of the periplasmic portion of outer membrane protein a (ompa) from capnocytophaga gingivalis”. X-ray diffraction, 2 ligands (CA, SO4), 11 pockets (best druggability 0.50). MolNFT v1 #138769 on…
- PDB
- 5WTL
- Type
- protein
- Length
- 1,023 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ompa family protein
- UniProt
- C2M2E7
- Ligands
- CA, SO4
- Pockets
- 11 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ompa family protein | protein | 258 | 32% helix, 9% strand | C2M2E7 |
| C | Ompa family protein | protein | 260 | 31% helix, 9% strand | C2M2E7 |
| D | Ompa family protein | protein | 247 | 30% helix, 9% strand | C2M2E7 |
Ligands and binding sites
- CA · Calcium ion · metal · 41 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.50 | 0.77 | 23 | empty |
| 2 | 162 | 0.49 | 0.77 | 22 | empty |
| 3 | 171 | 0.48 | 0.77 | 23 | empty |
| 4 | 157 | 0.48 | 0.77 | 20 | empty |
| 5 | 128 | 0.44 | 0.77 | 23 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 739 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 710 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 222 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 174 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5WTL · Crystal structure of the periplasmic portion 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 5WTL · PDBe 5WTL · UniProt C2M2E7
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