MolNFT v1 · #173557 · protein
Amip amidase-3 from thermus parvatiensis
7B3N · Cell wall hydrolase: “Amip amidase-3 from thermus parvatiensis”. X-ray diffraction, 4 ligands (ZN, NA, SO4), 9 pockets (best druggability 0.63). MolNFT v1 #173557 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7B3N
- Type
- protein
- Length
- 843 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell wall hydrolase
- UniProt
- H7GE39
- Ligands
- ZN, NA, SO4, CL
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell wall hydrolase | protein | 169 | 38% helix, 21% strand | H7GE39 |
| B | Cell wall hydrolase | protein | 170 | 38% helix, 21% strand | H7GE39 |
| C | Cell wall hydrolase | protein | 168 | 40% helix, 21% strand | H7GE39 |
| D, E | Cell wall hydrolase | protein | 168 | 40% helix, 21% strand | H7GE39 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 2 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, E
- CL · Chloride ion · ion · 2 copies · chains B, C, E
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.63 | 0.77 | 35 | ZN, GOL |
| 2 | 462 | 0.62 | 0.76 | 34 | GOL |
| 3 | 411 | 0.61 | 0.76 | 35 | ZN, GOL |
| 4 | 356 | 0.58 | 0.75 | 35 | GOL |
| 5 | 97 | 0.43 | 0.79 | 21 | NA |
Interfaces
4 interfaces between chains.
- A–B · 647 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 644 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 619 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 613 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7B3N · AmiP amidase-3 from Thermus parvatiensis · 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 H7GE39
- Elsewhere: RCSB PDB 7B3N · PDBe 7B3N · UniProt H7GE39
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