Research workbench
Crystal structure of mycobacterium tuberculosis S-adenosyl-L- homocysteine hydrolase in ternary complex with NAD and 3- deazaadenosine
Analyse Crystal structure of mycobacterium tuberculosis S-adenosyl-L- homocysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZIZ
- Type
- protein
- Length
- 1,940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P60176
- Ligands
- AD3, NAD
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 485 | 46% helix, 14% strand | P60176 |
Ligands and binding sites
- AD3 · 3-deaza-adenosine · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.88 | 0.93 | 67 | empty |
| 2 | 577 | 0.84 | 0.90 | 71 | NAD, AD3 |
| 3 | 541 | 0.84 | 0.90 | 71 | AD3, NAD |
| 4 | 568 | 0.84 | 0.90 | 74 | NAD, AD3 |
| 5 | 530 | 0.84 | 0.90 | 71 | AD3, NAD |
Interfaces
6 interfaces between chains.
- A–B · 3354 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3324 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1861 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1816 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 528 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2ZIZ · Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in… · 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 P60176
- Elsewhere: RCSB PDB 2ZIZ · PDBe 2ZIZ · UniProt P60176
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