Research workbench
Crystal structure of NGO0477 from neisseria gonorrhoeae
Analyse Crystal structure of NGO0477 from neisseria gonorrhoeae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KXA
- Type
- protein
- Length
- 522 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q5F9C2
- Ligands
- ASN, UNX, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative uncharacterized protein | protein | 131 | 58% helix, 8% strand | Q5F9C2 |
| B, D | Putative uncharacterized protein | protein | 130 | 58% helix, 8% strand | Q5F9C2 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, B, D, C
- UNX · Unknown atom or ion · ion · 22 copies · chains A, C, B, D
- CL · Chloride ion · ion · 13 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.81 | 0.83 | 72 | CL |
| 2 | 840 | 0.80 | 0.83 | 73 | CL |
| 3 | 83 | 0.34 | 0.74 | 15 | UNX |
| 4 | 89 | 0.32 | 0.73 | 12 | empty |
| 5 | 54 | 0.31 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2012 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 2005 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 684 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 614 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 3KXA · Crystal Structure of NGO0477 from Neisseria gonorrhoeae · the same entry in another collection · chain B against B, 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 Q5F9C2
- Elsewhere: RCSB PDB 3KXA · PDBe 3KXA · UniProt Q5F9C2
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