MolNFT v1 · #16153 · protein
Crystal structure of clostridium histolyticum colg collagenase collagen-binding domain 3B at 1.65 ångström resolution in presence of calcium
1NQD · Class 1 collagenase: “Crystal structure of clostridium histolyticum colg collagenase collagen-binding domain 3B at 1.65 ångström…”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.42). MolNFT v1 #16153 on GenesisL1…
- PDB
- 1NQD
- Type
- protein
- Length
- 225 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class 1 collagenase
- EC
- 3.4.24.3
- UniProt
- Q9S0X0
- Ligands
- CA
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Class 1 collagenase (EC 3.4.24.3) | protein | 111 | 3% helix, 61% strand | Q9S0X0 |
| B | Class 1 collagenase (EC 3.4.24.3) | protein | 114 | 3% helix, 61% strand | Q9S0X0 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.42 | 0.75 | 29 | empty |
| 2 | 60 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 719 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1NQD · Crystal structure of clostridium histolyticum colg collagenase collagen-binding domain 3B… · 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 Q9S0X0
- Elsewhere: RCSB PDB 1NQD · PDBe 1NQD · UniProt Q9S0X0
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