Research workbench
2.2 a resolution structure of vapbc-1 from nontypeable haemophilus influenzae
Analyse 2.2 a resolution structure of vapbc-1 from nontypeable haemophilus influenzae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NKL
- Type
- protein
- Length
- 413 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease vapc; Antitoxin VAPB1
- EC
- 3.1.-.-
- UniProt
- A0A2R3FUY7, A0A2S9RDZ4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease vapc (EC 3.1.-.-) | protein | 134 | 57% helix, 13% strand | A0A2R3FUY7 |
| B | Ribonuclease vapc (EC 3.1.-.-) | protein | 135 | 56% helix, 15% strand | A0A2R3FUY7 |
| C | Antitoxin VAPB1 | protein | 74 | 26% helix, 34% strand | A0A2S9RDZ4 |
| D | Antitoxin VAPB1 | protein | 70 | 26% helix, 36% strand | A0A2S9RDZ4 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.62 | 0.87 | 23 | empty |
| 2 | 63 | 0.31 | 0.76 | 13 | empty |
| 3 | 50 | 0.27 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1731 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1427 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1072 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NKL · 2.2 A resolution structure of VapBC-1 from nontypeable Haemophilus influenzae · 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 A0A2R3FUY7
- Every structure of UniProt A0A2S9RDZ4
- Elsewhere: RCSB PDB 6NKL · PDBe 6NKL · UniProt A0A2R3FUY7 · UniProt A0A2S9RDZ4
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