MolNFT v1 · #37912 · protein
The mutant A68C-D72C-nlq of deinococcus radiodurans nacylamino acid racemase
2GGH · N-acylamino acid racemase: “The mutant A68C-D72C-nlq of deinococcus radiodurans nacylamino acid racemase”. X-ray diffraction, 2 ligands (NLQ, MG), 8 pockets (best druggability 0.78). MolNFT v1 #37912 on GenesisL1: 3D structure…
- PDB
- 2GGH
- Type
- protein
- Length
- 1,460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylamino acid racemase
- EC
- 5.1.1.10
- UniProt
- Q9RYA6
- Ligands
- NLQ, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acylamino acid racemase (EC 5.1.1.10) | protein | 360 | 36% helix, 23% strand | Q9RYA6 |
| C, D | N-acylamino acid racemase (EC 5.1.1.10) | protein | 370 | 34% helix, 24% strand | Q9RYA6 |
Ligands and binding sites
- NLQ · N~2~-acetyl-L-glutamine · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.78 | 0.82 | 83 | empty |
| 2 | 768 | 0.77 | 0.82 | 86 | empty |
| 3 | 684 | 0.74 | 0.80 | 78 | MG |
| 4 | 199 | 0.70 | 0.88 | 40 | MG, NLQ |
| 5 | 201 | 0.70 | 0.87 | 39 | NLQ |
Interfaces
3 interfaces between chains.
- A–C · 1251 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1241 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 939 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2GGH · The mutant A68C-D72C-NLQ of Deinococcus Radiodurans Nacylamino acid racemase · 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 Q9RYA6
- Elsewhere: RCSB PDB 2GGH · PDBe 2GGH · UniProt Q9RYA6
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