MolNFT v1 · #54912 · protein
Crystal structure of apo collagenase G from clostridium histolyticum at 2.55 ångström resolution
2Y3U: “Crystal structure of apo collagenase G from clostridium histolyticum at 2.55 ångström resolution”. X-ray diffraction, 7 pockets (best druggability 0.53). MolNFT v1 #54912 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y3U
- Type
- protein
- Length
- 679 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase
- EC
- 3.4.24.3
- UniProt
- Q9X721
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase (EC 3.4.24.3) | protein | 679 | 55% helix, 11% strand | Q9X721 |
Ligands and binding sites
- P6G · Hexaethylene glycol · additive · chains A
- FLC · Citrate anion · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.53 | 0.81 | 23 | empty |
| 2 | 64 | 0.48 | 0.84 | 15 | empty |
| 3 | 109 | 0.39 | 0.75 | 15 | empty |
| 4 | 105 | 0.38 | 0.75 | 20 | empty |
| 5 | 75 | 0.34 | 0.75 | 18 | FLC |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 2Y3U · Crystal structure of apo collagenase G from Clostridium histolyticum at 2.55 Angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X721 · AlphaFold monomer V2.0 prediction for collagenase colg (Q9X721) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X721
- Elsewhere: RCSB PDB 2Y3U · PDBe 2Y3U · UniProt Q9X721
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