MolNFT v1 · #168088 · protein

Structure of the antibody fragment H2 in complex with HLA- A*02:01/P53R175H

6W51 · MHC class I antigen: “Structure of the antibody fragment H2 in complex with HLA- A*02:01/P53R175H”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.80). MolNFT v1 #168088 on GenesisL1: 3D structure, binding sites…

PDB: 6W51
Type: protein
Length: 3,264 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Cellular tumor antigen P53 peptide…
UniProt: U5YKE0, P61769, P04637
Ligands: PO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 12 distinct chains · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	268	26% helix, 39% strand	U5YKE0
B, K	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C, F, I, L	Cellular tumor antigen P53 peptide	protein	9	0% helix, 0% strand	P04637
D	MHC class I antigen	protein	274	25% helix, 39% strand	U5YKE0
E, H	Beta-2-microglobulin	protein	100	0% helix, 43% strand	P61769
G	MHC class I antigen	protein	272	25% helix, 37% strand	U5YKE0
J	MHC class I antigen	protein	275	26% helix, 40% strand	U5YKE0
M, O	Immunoglobulin heavy chain H2	protein	223	9% helix, 49% strand	—
N, P, R	Immunoglobulin light chain H2	protein	214	5% helix, 52% strand	—
Q	Immunoglobulin heavy chain H2	protein	221	8% helix, 51% strand	—
S	Immunoglobulin heavy chain H2	protein	222	9% helix, 50% strand	—
T	Immunoglobulin light chain H2	protein	210	5% helix, 53% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1153	0.80	0.81	116	empty
2	1071	0.78	0.80	110	empty
3	500	0.71	0.81	54	empty
4	910	0.71	0.76	80	empty
5	429	0.70	0.81	44	empty

Interfaces

35 interfaces between chains.

M–N · 2129 Å² buried · 15 hydrogen bonds · protein-protein
Q–R · 2083 Å² buried · 15 hydrogen bonds · protein-protein
O–P · 2055 Å² buried · 11 hydrogen bonds · protein-protein
S–T · 2053 Å² buried · 13 hydrogen bonds · protein-protein
J–K · 1423 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

6W51 · Structure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H · the same entry in another collection · chain T against T, 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 U5YKE0
Every structure of UniProt P61769
Every structure of UniProt P04637
Elsewhere: RCSB PDB 6W51 · PDBe 6W51 · UniProt U5YKE0 · UniProt P61769 · UniProt P04637

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