Research workbench
X-ray structure of ss-RNase-2 DES116-120
Analyse X-ray structure of ss-RNase-2 DES116-120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BFL
- Type
- protein
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiogenin-1
- UniProt
- B5XAZ0
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiogenin-1 | protein | 114 | 25% helix, 44% strand | B5XAZ0 |
| B | Angiogenin-1 | protein | 109 | 26% helix, 44% strand | B5XAZ0 |
| C | Angiogenin-1 | protein | 108 | 26% helix, 45% strand | B5XAZ0 |
| D | Angiogenin-1 | protein | 111 | 26% helix, 41% strand | B5XAZ0 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.77 | 0.81 | 84 | empty |
| 2 | 284 | 0.62 | 0.80 | 50 | empty |
| 3 | 65 | 0.29 | 0.74 | 19 | empty |
| 4 | 56 | 0.29 | 0.75 | 18 | empty |
| 5 | 55 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 785 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 780 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 712 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7BFL · X-ray structure of SS-RNase-2 des116-120 · the same entry in another collection · chain D against D, 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 B5XAZ0
- Elsewhere: RCSB PDB 7BFL · PDBe 7BFL · UniProt B5XAZ0
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