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Crystal structure of sulfamidase, crystal form L
Analyse Crystal structure of sulfamidase, crystal form L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MIV
- Type
- protein
- Length
- 3,851 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-sulphoglucosamine sulphohydrolase
- EC
- 3.10.1.1
- UniProt
- P51688
- Ligands
- NAG, CA, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 484 | 30% helix, 18% strand | P51688 |
| B | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 481 | 31% helix, 18% strand | P51688 |
| C | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 484 | 30% helix, 18% strand | P51688 |
| D | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 480 | 31% helix, 19% strand | P51688 |
| E | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 483 | 31% helix, 17% strand | P51688 |
| F | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 478 | 31% helix, 19% strand | P51688 |
| G | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 479 | 31% helix, 17% strand | P51688 |
| H | N-sulphoglucosamine sulphohydrolase (EC 3.10.1.1) | protein | 482 | 31% helix, 17% strand | P51688 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.84 | 0.96 | 51 | empty |
| 2 | 1040 | 0.82 | 0.83 | 126 | empty |
| 3 | 140 | 0.80 | 0.97 | 28 | empty |
| 4 | 1079 | 0.80 | 0.81 | 115 | empty |
| 5 | 144 | 0.80 | 0.96 | 26 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1974 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1947 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1874 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1817 Ų buried · 15 hydrogen bonds · protein-protein
- B–G · 940 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 glycan, 16 disulfide, 8 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
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 P51688
- Elsewhere: RCSB PDB 4MIV · PDBe 4MIV · UniProt P51688
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