MolNFT v1 · #88618 · protein

Complex of a B2 chicken MHC class I molecule and a 8MER chicken peptide

4D0D · Major histocompatibility complex class I glycoprotein…: “Complex of a B2 chicken MHC class I molecule and a 8MER chicken peptide”. X-ray diffraction, 19 pockets (best druggability 0.85). MolNFT v1 #88618 on GenesisL1: 3D structure…

PDB: 4D0D
Type: protein
Length: 1,509 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I glycoprotein haplotype B2; Beta-2-microglobulin…
UniProt: O46789, P21611, Q9DG07
Pockets: 19 · best druggability 0.85

Structure

x-ray diffraction · 7 distinct chains · 21% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex class I glycoprotein haplotype B2	protein	275	25% helix, 41% strand	O46789
B, H	Beta-2-microglobulin	protein	96	0% helix, 50% strand	P21611
C, F, I, L	Slp-76 adaptor protein	protein	8	0% helix, 0% strand	Q9DG07
D	Major histocompatibility complex class I glycoprotein haplotype B2	protein	272	25% helix, 42% strand	O46789
E, K	Beta-2-microglobulin	protein	97	0% helix, 49% strand	P21611
G	Major histocompatibility complex class I glycoprotein haplotype B2	protein	270	24% helix, 42% strand	O46789
J	Major histocompatibility complex class I glycoprotein haplotype B2	protein	274	25% helix, 43% strand	O46789

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.85	0.87	103	empty
2	712	0.83	0.87	87	empty
3	417	0.77	0.86	59	empty
4	381	0.74	0.84	47	empty
5	133	0.63	0.87	22	empty

Interfaces

18 interfaces between chains.

J–K · 1742 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1699 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1609 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1556 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1088 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4D0D · Complex of a B2 chicken MHC class I molecule and a 8MER chicken peptide · 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 O46789
Every structure of UniProt P21611
Every structure of UniProt Q9DG07
Elsewhere: RCSB PDB 4D0D · PDBe 4D0D · UniProt O46789 · UniProt P21611 · UniProt Q9DG07

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