MolNFT v1 · #70803 · protein
Crystal structure of holo glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant staphylococcus aureus MRSA252 at 1.7 ångström resolution
3LVF: “Crystal structure of holo glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant…”. X-ray diffraction, 1 ligand (NAD), 13 pockets (best druggability 0.80). MolNFT v1 #70803 on GenesisL1: 3D structure, binding…
- PDB
- 3LVF
- Type
- protein
- Length
- 1,341 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
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 338 | 28% helix, 29% strand | Q6GIL8 |
| R | Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12) | protein | 335 | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.80 | 0.82 | 122 | NAD |
| 2 | 1155 | 0.80 | 0.82 | 121 | NAD |
| 3 | 57 | 0.66 | 0.95 | 15 | empty |
| 4 | 453 | 0.66 | 0.79 | 56 | empty |
| 5 | 380 | 0.64 | 0.78 | 64 | empty |
Interfaces
6 interfaces between chains.
- P–O · 2186 Ų buried · 47 hydrogen bonds · protein-protein
- R–Q · 2138 Ų buried · 47 hydrogen bonds · protein-protein
- R–O · 1482 Ų buried · 27 hydrogen bonds · protein-protein
- P–Q · 1472 Ų buried · 25 hydrogen bonds · protein-protein
- O–Q · 603 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3LVF · Crystal Structure of holo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from… · 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 3LVF · PDBe 3LVF · UniProt Q6GIL8
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