MolNFT v1 · #151957 · protein
Crystal structure of neanderthal glycine decarboxylase (P-protein)
6I34: “Crystal structure of neanderthal glycine decarboxylase (P-protein)”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.86). MolNFT v1 #151957 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6I34
- Type
- protein
- Length
- 3,813 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neanderthal glycine decarboxylase
- EC
- 1.4.4.2
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neanderthal glycine decarboxylase (EC 1.4.4.2) | protein | 953 | 44% helix, 12% strand | — |
| B | Neanderthal glycine decarboxylase (EC 1.4.4.2) | protein | 954 | 44% helix, 12% strand | — |
| D | Neanderthal glycine decarboxylase (EC 1.4.4.2) | protein | 953 | 44% helix, 12% strand | — |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.86 | 0.88 | 74 | PEG |
| 2 | 1125 | 0.85 | 0.86 | 124 | PEG, EDO |
| 3 | 1121 | 0.85 | 0.86 | 117 | EDO |
| 4 | 1119 | 0.84 | 0.85 | 108 | PEG |
| 5 | 60 | 0.71 | 0.98 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3900 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 3863 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6I34 · Crystal structure of Neanderthal glycine decarboxylase (P-protein) · 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 6I34 · PDBe 6I34
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