MolNFT v1 · #168066 · protein

NMR-driven structure of KRAS4B-GTP homodimer on a lipid bilayer nanodisc

6W4E · Apolipoprotein a-I: “NMR-driven structure of KRAS4B-GTP homodimer on a lipid bilayer nanodisc”. Solution nmr, 4 ligands (PCW, 17F, GSP), 5 pockets (best druggability 0.77). MolNFT v1 #168066 on GenesisL1: 3D structure, binding sites…

PDB: 6W4E
Type: protein
Length: 764 residues
Chains: 4
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apolipoprotein a-I; GTPase KRAS
UniProt: P02647, P01116
Ligands: PCW, 17F, GSP, MG
Pockets: 5 · best druggability 0.77

Structure

solution nmr · 2 distinct chains · 67% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Apolipoprotein a-I	protein	198	96% helix, 0% strand	P02647
B, C	GTPase KRAS	protein	184	36% helix, 24% strand	P01116

Ligands and binding sites

PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 64 copies · chains A, C, D, B
17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 16 copies · chains A, C, D, B
GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains B, C
MG · Magnesium ion · metal · 2 copies · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	812	0.77	0.81	72	empty
2	173	0.59	0.82	32	GSP
3	150	0.54	0.81	30	GSP
4	69	0.38	0.79	15	empty
5	52	0.28	0.75	14	empty

Interfaces

2 interfaces between chains.

A–D · 3722 Å² buried · 62 hydrogen bonds · protein-protein
B–C · 858 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6W4E · NMR-driven structure of KRAS4B-GTP homodimer on a lipid bilayer nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
P02647 · AlphaFold monomer V2.0 prediction for apolipoprotein a-I (P02647) · a predicted model of the same protein · chain A against A, TM-score 0.58

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 P02647
Every structure of UniProt P01116
Elsewhere: RCSB PDB 6W4E · PDBe 6W4E · UniProt P02647 · UniProt P01116

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