Research workbench
Crystal structure of H178N mutant of glyceraldehyde-3-phosphate- dehydrogenase 1 (GAPDH 1) from staphylococcus aureus MRSA252 complexed with NAD at 2.0 ångström resolution.
Analyse Crystal structure of H178N mutant of glyceraldehyde-3-phosphate- dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LC1
- Type
- protein
- Length
- 1,340 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase 1
- EC
- 1.2.1.12
- UniProt
- Q6GIL8
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, R | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 336 | 28% helix, 29% strand | Q6GIL8 |
| O, Q | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 334 | 28% helix, 29% strand | Q6GIL8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains P, Q, R, O
- GOL · Glycerol · additive · chains P, R, O, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.80 | 0.81 | 117 | NAD |
| 2 | 554 | 0.74 | 0.82 | 61 | NAD |
| 3 | 528 | 0.73 | 0.82 | 51 | NAD |
| 4 | 407 | 0.70 | 0.82 | 60 | GOL |
| 5 | 454 | 0.66 | 0.79 | 54 | empty |
Interfaces
6 interfaces between chains.
- P–O · 2199 Ų buried · 48 hydrogen bonds · protein-protein
- R–Q · 2134 Ų buried · 49 hydrogen bonds · protein-protein
- R–O · 1479 Ų buried · 24 hydrogen bonds · protein-protein
- P–Q · 1477 Ų buried · 25 hydrogen bonds · protein-protein
- O–Q · 601 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3LC1 · Crystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1 (GAPDH 1)… · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q6GIL8 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase 1 (Q6GIL8) · a predicted model of the same protein · chain O 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 Q6GIL8
- Elsewhere: RCSB PDB 3LC1 · PDBe 3LC1 · UniProt Q6GIL8
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