MolNFT v1 · #121111 · protein
Crystal structure of avidin complex with a ferrocene biotin derivative
5HLM: “Crystal structure of avidin complex with a ferrocene biotin derivative”. X-ray diffraction, 2 ligands (B9F, NAG), 9 pockets (best druggability 0.68). MolNFT v1 #121111 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HLM
- Type
- protein
- Length
- 461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avidin
- UniProt
- P02701
- Ligands
- B9F, NAG
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Avidin | protein | 114 | 5% helix, 54% strand | P02701 |
| B | Avidin | protein | 108 | 6% helix, 54% strand | P02701 |
| C | Avidin | protein | 118 | 5% helix, 51% strand | P02701 |
| D | Avidin | protein | 121 | 5% helix, 50% strand | P02701 |
Ligands and binding sites
- B9F · [(1,2,3,4,5-eta)-cyclopentadienyl]{(1,2,3,4,5-eta)-1-[1-hydroxy-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentyl]cyclopentadienyl}iron · ligand · 4 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.68 | 0.82 | 47 | empty |
| 2 | 184 | 0.64 | 0.84 | 28 | B9F |
| 3 | 157 | 0.63 | 0.85 | 20 | B9F |
| 4 | 109 | 0.60 | 0.86 | 18 | B9F |
| 5 | 140 | 0.59 | 0.83 | 19 | B9F |
Interfaces
6 interfaces between chains.
- C–D · 1908 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1601 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 592 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 P02701
- Elsewhere: RCSB PDB 5HLM · PDBe 5HLM · UniProt P02701
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