MolNFT v1 · #121670 · protein
Azurin T30R1, crystal form II
5I28: “Azurin T30R1, crystal form II”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.75). MolNFT v1 #121670 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I28
- Type
- protein
- Length
- 2,048 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Azurin
- UniProt
- P00282
- Ligands
- CU
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Azurin | protein | 128 | 20% helix, 34% strand | P00282 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.75 | 0.84 | 60 | empty |
| 2 | 534 | 0.74 | 0.82 | 74 | empty |
| 3 | 477 | 0.72 | 0.82 | 74 | empty |
| 4 | 786 | 0.70 | 0.76 | 64 | empty |
| 5 | 212 | 0.69 | 0.86 | 28 | empty |
Interfaces
28 interfaces between chains.
- I–L · 599 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 5 hydrogen bonds · protein-protein
- B–P · 546 Ų buried · 6 hydrogen bonds · protein-protein
- H–P · 499 Ų buried · 9 hydrogen bonds · protein-protein
- C–K · 497 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 16 modified (disulfide, nonstandard).
Compared structures
- 5I28 · Azurin T30R1, crystal form II · the same entry in another collection · chain K against K, 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 P00282
- Elsewhere: RCSB PDB 5I28 · PDBe 5I28 · UniProt P00282
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