MolNFT v1 · #92453 · protein

Crystal structure of HLA B2705-KK10-L6M

4G8I · HLA class I histocompatibility antigen, B-27 alpha chain: “Crystal structure of HLA B2705-KK10-L6M”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #92453 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4G8I
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-27 alpha chain; Beta-2-microglobulin; Gag…
UniProt: P03989, P61769, Q9YNZ1
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-27 alpha chain	protein	276	28% helix, 39% strand	P03989
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Gag protein	protein	10	0% helix, 0% strand	Q9YNZ1

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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	667	0.69	0.77	56	TRS
2	89	0.65	0.90	21	empty
3	134	0.48	0.79	20	empty
4	75	0.42	0.80	22	empty
5	76	0.37	0.77	14	empty

Interfaces

2 interfaces between chains.

A–B · 1303 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 939 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4G8I · Crystal Structure of HLA B2705-KK10-L6M · 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 0.99

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 P03989
Every structure of UniProt P61769
Every structure of UniProt Q9YNZ1
Elsewhere: RCSB PDB 4G8I · PDBe 4G8I · UniProt P03989 · UniProt P61769 · UniProt Q9YNZ1

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