MolNFT v1 · #60075 · protein

Crystal structure of H-2DB in complex with chimeric GP100

3CH1 · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of H-2DB in complex with chimeric GP100”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.68). MolNFT v1 #60075 on GenesisL1: 3D…

PDB: 3CH1
Type: protein
Length: 1,522 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; Nonameric…
UniProt: P01899, P01887
Ligands: SO4
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 6 distinct chains · 22% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	274	24% helix, 39% strand	P01899
B, E, H, K	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	273	25% helix, 39% strand	P01899
G	H-2 class I histocompatibility antigen, D-B alpha chain	protein	271	25% helix, 40% strand	P01899
J	H-2 class I histocompatibility antigen, D-B alpha chain	protein	272	25% helix, 39% strand	P01899
C, F, I, L	Nonameric peptide chimeric GP100	protein	9	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, D, J, L
GOL · Glycerol · additive · 26 copies · chains A, B, D, E, G, H, J, K, I

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

Pockets

20 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	820	0.68	0.75	68	GOL
2	685	0.65	0.74	67	GOL
3	609	0.64	0.75	49	GOL
4	624	0.64	0.74	45	GOL
5	163	0.46	0.76	34	GOL

Interfaces

10 interfaces between chains.

G–H · 1264 Å² buried · 23 hydrogen bonds · protein-protein
J–K · 1264 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1247 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1247 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 951 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3CH1 · Crystal structure of H-2Db in complex with chimeric gp100 · 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
Elsewhere: RCSB PDB 3CH1 · PDBe 3CH1 · UniProt P01899 · UniProt P01887

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