MolNFT v1 · #52421 · protein
Does a fast nuclear magnetic resonance spectroscopy- and X-ray crystallography hybrid approach provide reliable structural information of ligand-protein complexes? a case study of metalloproteinases.
2W0D · Macrophage metalloelastase: “Does a fast nuclear magnetic resonance spectroscopy- and X-ray crystallography hybrid approach provide…”. X-ray diffraction, 5 ligands (CGS, CA, ZN), 7 pockets (best druggability 0.76). MolNFT v1 #52421…
- PDB
- 2W0D
- Type
- protein
- Length
- 634 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage metalloelastase
- EC
- 3.4.24.65
- UniProt
- P39900
- Ligands
- CGS, CA, ZN, NA, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Macrophage metalloelastase (EC 3.4.24.65) | protein | 158 | 25% helix, 17% strand | P39900 |
| C, D | Macrophage metalloelastase (EC 3.4.24.65) | protein | 159 | 25% helix, 17% strand | P39900 |
Ligands and binding sites
- CGS · N-hydroxy-2(R)-[[(4-methoxyphenyl)sulfonyl](3-picolyl)amino]-3-methylbutanamide hydrochloride · ligand · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 10 copies · chains A, D, B, C
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · 2 copies · chains C, D
- ACT · Acetate ion · additive · 7 copies · chains A, D, C, B
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 | 791 | 0.76 | 0.80 | 70 | ZN, CGS |
| 2 | 546 | 0.74 | 0.82 | 70 | ZN, NA, ACT, CGS |
| 3 | 470 | 0.65 | 0.78 | 42 | empty |
| 4 | 194 | 0.59 | 0.81 | 26 | ZN, CGS |
| 5 | 84 | 0.37 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–D · 553 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 139 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2W0D · Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid… · 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 P39900
- Elsewhere: RCSB PDB 2W0D · PDBe 2W0D · UniProt P39900
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.