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Crystal structure of H-2DB with the GAP501 peptide (sql)

Analyse Crystal structure of H-2DB with the GAP501 peptide (sql) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WLI
Type: protein
Length: 1,534 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; GAP50…
UniProt: P01899, P01887, A0A0Y9W4B5
Ligands: PO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G, J	H-2 class I histocompatibility antigen, D-B alpha chain	protein	276	27% helix, 40% strand	P01899
B, E, K	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
C, F, I, L	GAP50 peptide	protein	9	0% helix, 0% strand	A0A0Y9W4B5
D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	277	27% helix, 39% strand	P01899
H	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887

Ligands and binding sites

PO4 · Phosphate ion · ion · 3 copies · chains A, G, H, J, K

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.83	0.84	91	empty
2	1059	0.82	0.83	94	empty
3	1033	0.81	0.83	86	empty
4	1049	0.81	0.82	96	empty
5	268	0.57	0.78	29	empty

Interfaces

17 interfaces between chains.

G–H · 1350 Å² buried · 21 hydrogen bonds · protein-protein
J–K · 1297 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1276 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1269 Å² buried · 22 hydrogen bonds · protein-protein
A–G · 977 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5WLI · Crystal Structure of H-2Db with the GAP501 peptide (SQL) · 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 P01899
Every structure of UniProt P01887
Every structure of UniProt A0A0Y9W4B5
Elsewhere: RCSB PDB 5WLI · PDBe 5WLI · UniProt P01899 · UniProt P01887 · UniProt A0A0Y9W4B5

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