MolNFT v1 · #145944 · protein

HLA-B*57:01 presenting lalltgvrw

6D2T · HLA class I histocompatibility antigen, B-57 alpha chain: “HLA-B*57:01 presenting lalltgvrw”. X-ray diffraction, 6 pockets (best druggability 0.67). MolNFT v1 #145944 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6D2T
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-57 alpha chain; Beta-2-microglobulin…
UniProt: P18465, P61769
Pockets: 6 · best druggability 0.67

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-57 alpha chain	protein	276	28% helix, 39% strand	P18465
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Leu-ala-leu-leu-thr-gly-val-arg-TRP	protein	9	0% helix, 0% strand	—

Pockets

6 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	622	0.67	0.77	54	empty
2	83	0.67	0.92	20	empty
3	129	0.48	0.79	24	empty
4	72	0.45	0.82	18	empty
5	83	0.38	0.77	16	empty

Interfaces

2 interfaces between chains.

A–B · 1407 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 876 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6D2T · HLA-B*57:01 presenting LALLTGVRW · 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 P18465
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6D2T · PDBe 6D2T · UniProt P18465 · UniProt P61769

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