MolNFT v1 · #190528 · protein
Collagenase from grimontia (vibrio) hollisae 1706B complexed with gly- pro-hyp
7XEB · Microbial collagenase: “Collagenase from grimontia (vibrio) hollisae 1706B complexed with gly- pro-hyp”. X-ray diffraction, 2 ligands (CA, ZN), 10 pockets (best druggability 0.54). MolNFT v1 #190528 on GenesisL1: 3D structure…
- PDB
- 7XEB
- Type
- protein
- Length
- 1,102 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microbial collagenase; Gly-pro-hyp peptide; Gly-pro-hyp-gly-pro-hyp peptide
- EC
- 3.4.24.3
- UniProt
- F7IZI6
- Ligands
- CA, ZN
- Pockets
- 10 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Microbial collagenase (EC 3.4.24.3) | protein | 533 | 64% helix, 6% strand | F7IZI6 |
| C, D, G, H | Gly-pro-hyp peptide | protein | 3 | 0% helix, 0% strand | — |
| E, F, I, J | Gly-pro-hyp-gly-pro-hyp peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, C, D, B, G, H
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.54 | 0.87 | 21 | EDO |
| 2 | 184 | 0.46 | 0.75 | 26 | empty |
| 3 | 188 | 0.45 | 0.75 | 23 | empty |
| 4 | 70 | 0.44 | 0.82 | 18 | empty |
| 5 | 72 | 0.43 | 0.81 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–E · 387 Ų buried · 6 hydrogen bonds · protein-protein
- B–I · 384 Ų buried · 6 hydrogen bonds · protein-protein
- B–J · 367 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 354 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 330 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 6 disulfide (hydroxylation, disulfide).
Compared structures
- 7XEB · Collagenase from Grimontia (Vibrio) hollisae 1706B complexed with Gly-Pro-Hyp · the same entry in another collection · chain H against H, 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 F7IZI6
- Elsewhere: RCSB PDB 7XEB · PDBe 7XEB · UniProt F7IZI6
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