Research workbench
MMP13 catalytic domain complexed with 4-{[1-methyl-2,4-dioxo-6-(3- phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-YL]METHYL}BENZOIC acid
Analyse MMP13 catalytic domain complexed with 4-{[1-methyl-2,4-dioxo-6-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OZR
- Type
- protein
- Length
- 1,327 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- GG1, HAE, CA, ZN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Collagenase 3 (EC 3.4.24.-) | protein | 167 | 23% helix, 17% strand | P45452 |
| D | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 23% helix, 17% strand | P45452 |
| E | Collagenase 3 (EC 3.4.24.-) | protein | 164 | 25% helix, 17% strand | P45452 |
| G | Collagenase 3 (EC 3.4.24.-) | protein | 166 | 23% helix, 17% strand | P45452 |
| H | Collagenase 3 (EC 3.4.24.-) | protein | 163 | 24% helix, 17% strand | P45452 |
Ligands and binding sites
- GG1 · 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- HAE · Acetohydroxamic acid · ligand · 4 copies · chains C, D, E, F
- CA · Calcium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.83 | 0.84 | 131 | GG1 |
| 2 | 1084 | 0.74 | 0.76 | 94 | GG1, HAE |
| 3 | 890 | 0.72 | 0.77 | 76 | GG1, HAE |
| 4 | 281 | 0.72 | 0.86 | 50 | empty |
| 5 | 570 | 0.71 | 0.79 | 70 | GG1 |
Interfaces
18 interfaces between chains.
- C–E · 1213 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1100 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 770 Ų buried · 15 hydrogen bonds · protein-protein
- B–H · 767 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 400 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2OZR · MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1… · 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 P45452
- Elsewhere: RCSB PDB 2OZR · PDBe 2OZR · UniProt P45452
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