MolNFT v1 · #69499 · protein

Crystal structure of C151S+H178N mutant of glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from staphylococcus aureus MRSA252 complexed with NAD at 2.2 ångström resolution

3KSD: “Crystal structure of C151S+H178N mutant of glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from…”. X-ray diffraction, 1 ligand (NAD), 13 pockets (best druggability 0.80). MolNFT v1 #69499 on GenesisL1: 3D structure, binding…

PDB: 3KSD
Type: protein
Length: 1,332 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 · 4 distinct chains · 29% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12)	protein	333	29% helix, 29% strand	Q6GIL8
R	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12)	protein	333	29% helix, 29% strand	Q6GIL8
O	Glyceraldehyde-3-phosphate dehydrogenase 1 (EC 1.2.1.12)	protein	332	29% helix, 27% strand	Q6GIL8
P	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 Q, P, 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1162	0.80	0.82	117	NAD
2	937	0.77	0.79	110	empty
3	437	0.73	0.83	60	NAD
4	393	0.72	0.83	49	NAD
5	82	0.47	0.83	20	empty

Interfaces

6 interfaces between chains.

Q–R · 2125 Å² buried · 44 hydrogen bonds · protein-protein
O–P · 2088 Å² buried · 38 hydrogen bonds · protein-protein
R–O · 1510 Å² buried · 30 hydrogen bonds · protein-protein
Q–P · 1476 Å² buried · 29 hydrogen bonds · protein-protein
Q–O · 641 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3KSD · Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosphate dehydrogenase 1… · the same entry in another collection · chain P against P, 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 Q 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 3KSD · PDBe 3KSD · UniProt Q6GIL8

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