Research workbench
Crystal structure of human mmp-13 complexed with an amino-2-indanol compound
Analyse Crystal structure of human mmp-13 complexed with an amino-2-indanol compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LJZ
- Type
- protein
- Length
- 653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- LA3, CA, ZN, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 161 | 25% helix, 17% strand | P45452 |
| B, C, D | Collagenase 3 (EC 3.4.24.-) | protein | 164 | 24% helix, 18% strand | P45452 |
Ligands and binding sites
- LA3 · (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide · ligand · 4 copies · chains A, B, D, C
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.81 | 0.82 | 153 | LA3 |
| 2 | 278 | 0.72 | 0.86 | 47 | empty |
| 3 | 147 | 0.55 | 0.81 | 28 | LA3 |
| 4 | 173 | 0.54 | 0.79 | 27 | ZN, LA3 |
| 5 | 67 | 0.34 | 0.76 | 19 | EPE |
Interfaces
5 interfaces between chains.
- A–D · 806 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 764 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 302 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 252 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 109 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3LJZ · Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound · the same entry in another collection · chain B against B, 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 3LJZ · PDBe 3LJZ · UniProt P45452
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