MolNFT v1 · #80536 · protein
Crystal structure of a glycine cleavage system H protein (gcvh) from mycobacterium marinum
3TZU · Glycine cleavage system H protein 1: “Crystal structure of a glycine cleavage system H protein (gcvh) from mycobacterium marinum”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #80536 on GenesisL1: 3D structure…
- PDB
- 3TZU
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine cleavage system H protein 1
- UniProt
- B2HKH2
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycine cleavage system H protein 1 | protein | 127 | 19% helix, 37% strand | B2HKH2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.76 | 0.98 | 29 | EDO |
| 2 | 89 | 0.74 | 0.96 | 28 | EDO |
| 3 | 700 | 0.71 | 0.78 | 97 | PEG |
| 4 | 53 | 0.41 | 0.82 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 662 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 661 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 286 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 279 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3TZU · Crystal structure of a glycine cleavage system H protein (GCVH) from Mycobacterium marinum · the same entry in another collection · chain D against D, 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 B2HKH2
- Elsewhere: RCSB PDB 3TZU · PDBe 3TZU · UniProt B2HKH2
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