Research workbench

KIR3DL1001 in complex with HLA-A24:02 presenting the rypltfgw peptide

Analyse KIR3DL1*001 in complex with HLA-A*24:02 presenting the rypltfgw peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K80
Type: protein
Length: 1,333 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Arg-tyr-pro-leu-thr-phe-gly-TRP; Killer cell…
UniProt: A0A411J078, P61769, P43629
Ligands: NAG
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 9% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I antigen	protein	276	26% helix, 39% strand	A0A411J078
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Arg-tyr-pro-leu-thr-phe-gly-TRP	protein	8	0% helix, 0% strand	—
G	Killer cell immunoglobulin-like receptor 3DL1	protein	290	3% helix, 50% strand	P43629
H	Killer cell immunoglobulin-like receptor 3DL1	protein	275	2% helix, 49% strand	P43629

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains G, H
ACT · Acetate ion · additive · 5 copies · chains A, B, D, E
FMT · Formic acid · additive · chains A

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	841	0.77	0.81	88	empty
2	616	0.72	0.80	71	empty
3	584	0.68	0.77	55	FMT
4	552	0.67	0.77	48	ACT
5	673	0.65	0.75	60	empty

Interfaces

12 interfaces between chains.

A–B · 1477 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1454 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 970 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 952 Å² buried · 15 hydrogen bonds · protein-protein
A–G · 909 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

7K80 · KIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide · the same entry in another collection · chain H against H, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
P43629 · AlphaFold monomer V2.0 prediction for killer cell immunoglobulin-like receptor 3DL1… · a predicted model of the same protein · chain G against A, TM-score 0.96

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 A0A411J078
Every structure of UniProt P61769
Every structure of UniProt P43629
Elsewhere: RCSB PDB 7K80 · PDBe 7K80 · UniProt A0A411J078 · UniProt P61769 · UniProt P43629

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