MolNFT v1 · #136961 · protein
Crystal structure of S-adenosyl-L-homocysteine hydrolase from naegleria fowleri with bound NAD and adenosine
5V96: “Crystal structure of S-adenosyl-L-homocysteine hydrolase from naegleria fowleri with bound NAD and adenosine”. X-ray diffraction, 3 ligands (NAD, ADN, PO4), 16 pockets (best druggability 0.89). MolNFT v1 #136961 on GenesisL1: 3D…
- PDB
- 5V96
- Type
- protein
- Length
- 1,861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosyl-L-homocysteine hydrolase
- Ligands
- NAD, ADN, PO4
- Pockets
- 16 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosyl-L-homocysteine hydrolase | protein | 467 | 46% helix, 15% strand | — |
| B | S-adenosyl-L-homocysteine hydrolase | protein | 464 | 47% helix, 15% strand | — |
| C, D | S-adenosyl-L-homocysteine hydrolase | protein | 465 | 48% helix, 15% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ADN · Adenosine · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.89 | 0.90 | 78 | EDO |
| 2 | 744 | 0.86 | 0.89 | 93 | NAD, ADN, PO4, EDO |
| 3 | 777 | 0.85 | 0.88 | 103 | EDO, NAD, ADN, PO4 |
| 4 | 1136 | 0.83 | 0.84 | 119 | NAD, ADN, PO4, EDO |
| 5 | 1183 | 0.82 | 0.83 | 123 | EDO, NAD, ADN, PO4 |
Interfaces
6 interfaces between chains.
- A–B · 3025 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 3021 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1855 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1810 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 409 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5V96 · Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with… · 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
- Elsewhere: RCSB PDB 5V96 · PDBe 5V96
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