MolNFT v1 · #120947 · protein
Crystal structure of upa in complex with a camelid-derived antibody fragment
5HGG · Urokinase-type plasminogen activator: “Crystal structure of upa in complex with a camelid-derived antibody fragment”. X-ray diffraction, 2 ligands (TWN, SO4), 8 pockets (best druggability 0.85). MolNFT v1 #120947 on GenesisL1: 3D…
- PDB
- 5HGG
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Camelid derived antibody fragment, NB4
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- TWN, SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 246 | 11% helix, 37% strand | P00749 |
| S | Camelid derived antibody fragment, NB4 | protein | 128 | 5% helix, 47% strand | — |
| T | Camelid derived antibody fragment, NB4 | protein | 127 | 5% helix, 47% strand | — |
Ligands and binding sites
- TWN · (3S)-3-[(2S,3S,4R)-3,4-dimethyltetrahydrofuran-2-yl]butyl laurate · ligand · 3 copies · chains A, B, S, T
- SO4 · Sulfate ion · ion · 2 copies · chains B, S
- GOL · Glycerol · additive · 5 copies · chains A, S, B, T
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.85 | 0.87 | 72 | TWN |
| 2 | 81 | 0.47 | 0.82 | 19 | empty |
| 3 | 125 | 0.45 | 0.77 | 19 | empty |
| 4 | 109 | 0.43 | 0.77 | 19 | GOL |
| 5 | 59 | 0.36 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–T · 1033 Ų buried · 32 hydrogen bonds · protein-protein
- B–S · 1020 Ų buried · 31 hydrogen bonds · protein-protein
- A–S · 523 Ų buried · 6 hydrogen bonds · protein-protein
- B–T · 490 Ų buried · 3 hydrogen bonds · protein-protein
- S–T · 311 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5HGG · Crystal structure of uPA in complex with a camelid-derived antibody fragment · 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 P00749
- Elsewhere: RCSB PDB 5HGG · PDBe 5HGG · UniProt P00749
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