MolNFT v1 · #105004 · protein

Crystal structure of HLA B*0801 in complex with hskkkcdel and DD31 TCR

4QRP · HLA class I histocompatibility antigen, B-8 alpha chain: “Crystal structure of HLA B*0801 in complex with hskkkcdel and DD31 TCR”. X-ray diffraction, 2 ligands (NA, IOD), 20 pockets (best druggability 0.76). MolNFT v1 #105004 on…

PDB: 4QRP
Type: protein
Length: 2,106 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-8 alpha chain; Beta-2-microglobulin; NS3-4A…
UniProt: P30460, P61769, X2G898
Ligands: NA, IOD
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 7 distinct chains · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	HLA class I histocompatibility antigen, B-8 alpha chain	protein	276	26% helix, 38% strand	P30460
B	Beta-2-microglobulin	protein	99	0% helix, 40% strand	P61769
C, H	NS3-4A protein	protein	9	0% helix, 0% strand	X2G898
D, J	DD31 TCR alpha chain	protein	203	4% helix, 42% strand	—
E, I, L	DD31 TCR beta chain	protein	243	7% helix, 49% strand	—
G	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
K	DD31 TCR alpha chain	protein	202	3% helix, 41% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains E, F, G, L
IOD · Iodide ion · ion · 12 copies · chains D, E, G, F, A, I, B, J, K, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1011	0.76	0.79	97	IOD, NA
2	1150	0.75	0.78	102	empty
3	974	0.73	0.76	66	empty
4	376	0.70	0.83	46	IOD
5	484	0.70	0.80	60	empty

Interfaces

26 interfaces between chains.

I–J · 2129 Å² buried · 27 hydrogen bonds · protein-protein
K–L · 2020 Å² buried · 25 hydrogen bonds · protein-protein
D–E · 1961 Å² buried · 22 hydrogen bonds · protein-protein
F–G · 1375 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1353 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

4QRP · Crystal Structure of HLA B*0801 in complex with HSKKKCDEL and DD31 TCR · the same entry in another collection · chain L against L, TM-score 1.00

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 P30460
Every structure of UniProt P61769
Every structure of UniProt X2G898
Elsewhere: RCSB PDB 4QRP · PDBe 4QRP · UniProt P30460 · UniProt P61769 · UniProt X2G898

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