MolNFT v1 · #173983 · protein

3H4-Fab HLA-E-VL9 co-complex

7BH8 · HLA class I histocompatibility antigen, alpha chain E: “3H4-Fab HLA-E-VL9 co-complex”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.71). MolNFT v1 #173983 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7BH8
Type: protein
Length: 1,624 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, alpha chain E; Beta-2-microglobulin; 3H4 Fab…
UniProt: P13747, P61769
Ligands: CA
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 8 distinct chains · 14% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, alpha chain E	protein	276	28% helix, 39% strand	P13747
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	HLA class I histocompatibility antigen, alpha chain E	protein	261	26% helix, 36% strand	P13747
D	Beta-2-microglobulin	protein	98	0% helix, 49% strand	P61769
G	3H4 Fab heavy chain	protein	225	9% helix, 52% strand	—
H, F	3H4 Fab light chain	protein	214	6% helix, 50% strand	—
E	3H4 Fab heavy chain	protein	218	9% helix, 53% strand	—
P, Q	VL9 leader peptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · chains G, H
GOL · Glycerol · additive · 10 copies · chains A, B, C, G, H, F

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	691	0.71	0.78	62	GOL
2	676	0.68	0.76	64	GOL
3	281	0.61	0.80	38	empty
4	289	0.61	0.79	27	GOL
5	293	0.59	0.78	25	empty

Interfaces

15 interfaces between chains.

G–H · 2108 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1934 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1356 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1257 Å² buried · 18 hydrogen bonds · protein-protein
C–Q · 939 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

7BH8 · 3H4-Fab HLA-E-VL9 co-complex · the same entry in another collection · chain H against H, 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 P13747
Every structure of UniProt P61769
Elsewhere: RCSB PDB 7BH8 · PDBe 7BH8 · UniProt P13747 · UniProt P61769

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