MolNFT v1 · #103920 · protein

Crystal structure of H2KB-Q600F complex

4PV8 · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H2KB-Q600F complex”. X-ray diffraction, 11 pockets (best druggability 0.65). MolNFT v1 #103920 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4PV8
Type: protein
Length: 770 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; S598…
UniProt: P01901, P01887
Pockets: 11 · best druggability 0.65

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	H-2 class I histocompatibility antigen, K-B alpha chain	protein	278	27% helix, 39% strand	P01901
B, D	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
E, F	S598 peptide modified Q600F	protein	8	0% helix, 0% strand	—

Ligands and binding sites

PG4 · Tetraethylene glycol · additive · chains C, F
ACT · Acetate ion · additive · chains C, D

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

Pockets

11 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	684	0.65	0.74	55	empty
2	645	0.64	0.74	53	empty
3	203	0.55	0.79	34	empty
4	185	0.49	0.76	31	ACT
5	129	0.49	0.79	18	empty

Interfaces

5 interfaces between chains.

C–D · 1229 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1219 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 914 Å² buried · 21 hydrogen bonds · protein-protein
A–E · 909 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 717 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

4PV8 · Crystal Structure of H2Kb-Q600F complex · the same entry in another collection · chain F against F, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B 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 P01901
Every structure of UniProt P01887
Elsewhere: RCSB PDB 4PV8 · PDBe 4PV8 · UniProt P01901 · UniProt P01887

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