MolNFT v1 · #170275 · protein

Crystal structure of HLA-B2709 complexed with the nona-peptide me

6Y29 · Lymphocyte antigen HLA-B27: “Crystal structure of HLA-B2709 complexed with the nona-peptide me”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #170275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y29
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lymphocyte antigen HLA-B27; Beta-2-microglobulin; Me
UniProt: A0A2R7Z5J3, P61769
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lymphocyte antigen HLA-B27	protein	276	27% helix, 40% strand	A0A2R7Z5J3
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Me	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	641	0.68	0.77	56	GOL
2	81	0.67	0.93	19	empty
3	146	0.47	0.78	20	empty
4	67	0.42	0.81	21	empty
5	70	0.37	0.77	14	empty

Interfaces

2 interfaces between chains.

A–B · 1397 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 831 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6Y29 · Crystal structure of HLA-B2709 complexed with the nona-peptide mE · 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 A0A2R7Z5J3
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6Y29 · PDBe 6Y29 · UniProt A0A2R7Z5J3 · UniProt P61769

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