Research workbench
Crystal structure of porb from corynebacterium glutamicum ( crystal form III)
Analyse Crystal structure of porb from corynebacterium glutamicum ( crystal form III) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VQL
- Type
- protein
- Length
- 296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein CGL0972
- UniProt
- Q8NRS3
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein CGL0972 | protein | 76 | 66% helix, 3% strand | Q8NRS3 |
| B | Uncharacterized protein CGL0972 | protein | 73 | 66% helix, 3% strand | Q8NRS3 |
| D | Uncharacterized protein CGL0972 | protein | 71 | 70% helix, 6% strand | Q8NRS3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.60 | 0.85 | 27 | ZN |
| 2 | 78 | 0.55 | 0.86 | 18 | empty |
| 3 | 220 | 0.49 | 0.75 | 30 | empty |
| 4 | 60 | 0.30 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 657 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 299 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2VQL · Crystal structure of PorB from Corynebacterium glutamicum (crystal form III) · 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 Q8NRS3
- Elsewhere: RCSB PDB 2VQL · PDBe 2VQL · UniProt Q8NRS3
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