MolNFT v1 · #127767 · protein

Human leukocyte antigen class I A02 carrying llwnpgmav

5N6B · HLA class I histocompatibility antigen, a-2 alpha chain: “Human leukocyte antigen class I A02 carrying llwnpgmav”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.70). MolNFT v1 #127767 on GenesisL1: 3D structure…

PDB: 5N6B
Type: protein
Length: 770 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; NS5
UniProt: P01892, P61769, W8FN10
Ligands: SO4
Pockets: 12 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	26% helix, 40% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	NS5	protein	9	0% helix, 0% strand	W8FN10

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, D, E, F
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, D, E
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B, D
GOL · Glycerol · additive · chains E

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	723	0.70	0.77	61	EDO, PEG
2	720	0.69	0.77	62	EDO, SO4
3	411	0.64	0.78	43	SO4, EDO
4	86	0.46	0.81	20	EDO
5	102	0.44	0.78	24	EDO

Interfaces

7 interfaces between chains.

D–E · 1351 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1313 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 875 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 853 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 217 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5N6B · Human Leukocyte Antigen Class I A02 Carrying LLWNPGMAV · the same entry in another collection · chain F against F, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E 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 P01892
Every structure of UniProt P61769
Every structure of UniProt W8FN10
Elsewhere: RCSB PDB 5N6B · PDBe 5N6B · UniProt P01892 · UniProt P61769 · UniProt W8FN10

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