Research workbench
Anbu from hyphomicrobium sp. strain MC1 - sg: C2
Analyse Anbu from hyphomicrobium sp. strain MC1 - sg: C2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NYJ
- Type
- protein
- Length
- 3,735 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anbu
- UniProt
- F8JB59
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H, M, N, P | Anbu | protein | 234 | 33% helix, 29% strand | F8JB59 |
| C, D, K, L, O | Anbu | protein | 233 | 34% helix, 28% strand | F8JB59 |
| I | Anbu | protein | 232 | 34% helix, 27% strand | F8JB59 |
| J | Anbu | protein | 232 | 34% helix, 27% strand | F8JB59 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.75 | 0.98 | 15 | empty |
| 2 | 75 | 0.75 | 0.98 | 16 | empty |
| 3 | 810 | 0.75 | 0.79 | 96 | empty |
| 4 | 74 | 0.75 | 0.98 | 18 | empty |
| 5 | 68 | 0.74 | 0.98 | 14 | empty |
Interfaces
28 interfaces between chains.
- K–M · 2231 Ų buried · 26 hydrogen bonds · protein-protein
- C–N · 2175 Ų buried · 23 hydrogen bonds · protein-protein
- D–O · 2172 Ų buried · 32 hydrogen bonds · protein-protein
- E–P · 2085 Ų buried · 31 hydrogen bonds · protein-protein
- F–L · 2036 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5NYJ · Anbu from Hyphomicrobium sp. strain MC1 - SG: C2 · the same entry in another collection · chain L against L, 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 F8JB59
- Elsewhere: RCSB PDB 5NYJ · PDBe 5NYJ · UniProt F8JB59
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