Research workbench

Complex of a B14 chicken MHC class I molecule and a 9MER chicken peptide

Analyse Complex of a B14 chicken MHC class I molecule and a 9MER chicken peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CW1
Type: protein
Length: 755 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I glycoprotein haplotype B14…
UniProt: A0ZXM3, P21611
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 20% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex class I glycoprotein haplotype B14	protein	271	28% helix, 42% strand	A0ZXM3
B	Beta-2-microglobulin	protein	98	0% helix, 48% strand	P21611
C, F	Peptide	protein	9	0% helix, 0% strand	—
D	Major histocompatibility complex class I glycoprotein haplotype B14	protein	271	28% helix, 41% strand	A0ZXM3
E	Beta-2-microglobulin	protein	97	0% helix, 48% strand	P21611

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	772	0.78	0.82	99	empty
2	1033	0.78	0.80	105	empty
3	61	0.73	0.98	20	empty
4	186	0.61	0.83	22	empty
5	114	0.48	0.80	23	empty

Interfaces

9 interfaces between chains.

A–B · 1613 Å² buried · 28 hydrogen bonds · protein-protein
D–E · 1544 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1053 Å² buried · 19 hydrogen bonds · protein-protein
A–F · 1030 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 704 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4CW1 · Complex of a B14 chicken MHC class I molecule and a 9MER chicken peptide · the same entry in another collection · chain F against F, TM-score 1.00
P21611 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P21611) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 A0ZXM3
Every structure of UniProt P21611
Elsewhere: RCSB PDB 4CW1 · PDBe 4CW1 · UniProt A0ZXM3 · UniProt P21611

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