MolNFT v1 · #54997 · protein
Crystal structure of collagenase G from clostridium histolyticum in complex with isoamylphosphonyl-gly-pro-ala at 3.25 ångström resolution
2Y6I: “Crystal structure of collagenase G from clostridium histolyticum in complex with…”. X-ray diffraction, 2 ligands (IPI, ZN), 7 pockets (best druggability 0.55). MolNFT v1 #54997 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2Y6I
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase; Isoamylphosphonyl-gly-pro-ala
- EC
- 3.4.24.3
- UniProt
- Q9X721
- Ligands
- IPI, ZN
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase (EC 3.4.24.3) | protein | 671 | 58% helix, 11% strand | Q9X721 |
| B | Isoamylphosphonyl-gly-pro-ala | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- IPI · 3-methylbutylphosphonic acid · ligand · chains A, B
- ZN · Zinc ion · metal · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- FLC · Citrate anion · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
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 | 157 | 0.55 | 0.81 | 27 | empty |
| 2 | 59 | 0.49 | 0.85 | 14 | empty |
| 3 | 180 | 0.45 | 0.74 | 33 | empty |
| 4 | 114 | 0.37 | 0.74 | 21 | empty |
| 5 | 74 | 0.33 | 0.75 | 16 | FLC |
Interfaces
1 interface between chains.
- A–B · 243 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2Y6I · Crystal Structure of Collagenase G from Clostridium histolyticum in complex with… · 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 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 Q9X721
- Elsewhere: RCSB PDB 2Y6I · PDBe 2Y6I · UniProt Q9X721
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