MolNFT v1 · #187745 · protein

KRAS-G12D specific TCR9A in complex with C*05-gadgvgksl

7SU9 · TCR9A alpha chain: “KRAS-G12D specific TCR9A in complex with C*05-gadgvgksl”. X-ray diffraction, 2 ligands (MG, SO4), 8 pockets (best druggability 0.76). MolNFT v1 #187745 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7SU9
Type: protein
Length: 809 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TCR9A alpha chain; TCR9A beta chain; MHC class I antigen; Beta-2-microglobulin…
UniProt: A0A7T3RIQ2, P61769
Ligands: MG, SO4
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 13% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	TCR9A alpha chain	protein	186	5% helix, 45% strand	—
E	TCR9A beta chain	protein	241	7% helix, 51% strand	—
A	MHC class I antigen	protein	273	29% helix, 41% strand	A0A7T3RIQ2
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	KRAS-G12D-9MER with A18L substitution	protein	9	0% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains D, E, A
SO4 · Sulfate ion · ion · 2 copies · chains D, E
GOL · Glycerol · additive · 2 copies · chains E, A, C

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

Pockets

8 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	686	0.76	0.81	80	GOL, MG
2	361	0.66	0.80	42	empty
3	214	0.52	0.77	38	empty
4	140	0.43	0.76	17	empty
5	69	0.43	0.81	15	empty

Interfaces

5 interfaces between chains.

D–E · 2085 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1331 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 760 Å² buried · 19 hydrogen bonds · protein-protein
E–A · 495 Å² buried · 7 hydrogen bonds · protein-protein
D–A · 40 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

7SU9 · KRAS-G12D specific TCR9a in complex with C*05-GADGVGKSL · the same entry in another collection · chain D against D, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 A0A7T3RIQ2
Every structure of UniProt P61769
Elsewhere: RCSB PDB 7SU9 · PDBe 7SU9 · UniProt A0A7T3RIQ2 · UniProt P61769

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