MolNFT v1 · #12076 · protein

HLA-B*2709 bound to nona-peptide M9

1K5N · Major histocompatibility complex molecule HLA-B*2709: “HLA-B*2709 bound to nona-peptide M9”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #12076 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1K5N
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex molecule HLA-B*2709; Beta-2-microglobulin, light chain…
UniProt: P03989, P61769
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex molecule HLA-B*2709	protein	276	26% helix, 40% strand	P03989
B	Beta-2-microglobulin, light chain	protein	100	0% helix, 49% strand	P61769
C	Nonameric model peptide M9	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	668	0.69	0.77	60	GOL
2	65	0.66	0.94	21	empty
3	135	0.45	0.77	21	empty
4	70	0.41	0.80	21	empty
5	78	0.39	0.78	16	empty

Interfaces

2 interfaces between chains.

A–B · 1380 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 801 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1K5N · HLA-B*2709 bound to nona-peptide M9 · the same entry in another collection · chain A against A, 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 0.98

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 P03989
Every structure of UniProt P61769
Elsewhere: RCSB PDB 1K5N · PDBe 1K5N · UniProt P03989 · UniProt P61769

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