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Crystal structure of HLA B2705-KK10

Analyse Crystal structure of HLA B2705-KK10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4G9D
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-27 alpha chain; Beta-2-microglobulin; P24
UniProt: P03989, P61769, Q9YXW1
Pockets: 6 · best druggability 0.68

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-27 alpha chain	protein	276	27% helix, 39% strand	P03989
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	P24	protein	10	0% helix, 0% strand	Q9YXW1

Ligands and binding sites

GOL · Glycerol · additive · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	660	0.68	0.76	58	GOL
2	92	0.67	0.91	24	empty
3	114	0.49	0.81	20	empty
4	53	0.41	0.82	16	empty
5	77	0.37	0.77	16	empty

Interfaces

2 interfaces between chains.

A–B · 1310 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 950 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4G9D · Crystal Structure of HLA B2705-KK10 · the same entry in another collection · chain B against B, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · 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 P03989
Every structure of UniProt P61769
Every structure of UniProt Q9YXW1
Elsewhere: RCSB PDB 4G9D · PDBe 4G9D · UniProt P03989 · UniProt P61769 · UniProt Q9YXW1

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