Research workbench
Human sahh-like domain of human adenosylhomocysteinase 3
Analyse Human sahh-like domain of human adenosylhomocysteinase 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GVP
- Type
- protein
- Length
- 1,728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase 3
- EC
- 3.3.1.1
- UniProt
- Q96HN2
- Ligands
- NAD
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase 3 (EC 3.3.1.1) | protein | 433 | 44% helix, 16% strand | Q96HN2 |
| B | Adenosylhomocysteinase 3 (EC 3.3.1.1) | protein | 432 | 44% helix, 16% strand | Q96HN2 |
| C | Adenosylhomocysteinase 3 (EC 3.3.1.1) | protein | 432 | 45% helix, 16% strand | Q96HN2 |
| D | Adenosylhomocysteinase 3 (EC 3.3.1.1) | protein | 431 | 45% helix, 16% strand | Q96HN2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.84 | 0.85 | 73 | empty |
| 2 | 1197 | 0.80 | 0.81 | 112 | NAD |
| 3 | 1192 | 0.77 | 0.79 | 115 | NAD |
| 4 | 906 | 0.76 | 0.79 | 82 | empty |
| 5 | 551 | 0.76 | 0.83 | 69 | NAD |
Interfaces
6 interfaces between chains.
- B–D · 2427 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2353 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1441 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1308 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 5 hydrogen bonds · protein-protein
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 Q96HN2
- Elsewhere: RCSB PDB 3GVP · PDBe 3GVP · UniProt Q96HN2
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