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Crystal structure of TCR C7 in complex with hcmv nlv epitope presented by HLA-A2

Analyse Crystal structure of TCR C7 in complex with hcmv nlv epitope presented by HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D2L
Type: protein
Length: 3,198 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; C7 TCR…
UniProt: P01892, P61769
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 15 distinct chains · 8% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	HLA class I histocompatibility antigen, a-2 alpha chain	protein	274	26% helix, 36% strand	P01892
B	Beta-2-microglobulin	protein	99	0% helix, 36% strand	P61769
I	C7 TCR alpha chain	protein	185	2% helix, 36% strand	—
J	C7 TCR beta chain	protein	226	3% helix, 37% strand	—
Q, U, T, R	Asn-leu-val-pro-met-val-ala-thr-val	protein	9	0% helix, 0% strand	—
G	HLA class I histocompatibility antigen, a-2 alpha chain	protein	270	23% helix, 37% strand	P01892
H	Beta-2-microglobulin	protein	96	0% helix, 38% strand	P61769
K	C7 TCR alpha chain	protein	192	2% helix, 35% strand	—
L	C7 TCR beta chain	protein	226	2% helix, 36% strand	—
M	HLA class I histocompatibility antigen, a-2 alpha chain	protein	273	22% helix, 36% strand	P01892
N, D	Beta-2-microglobulin	protein	100	0% helix, 46% strand	P61769
O	C7 TCR alpha chain	protein	187	0% helix, 33% strand	—
P	C7 TCR beta chain	protein	235	5% helix, 40% strand	—
E	C7 TCR alpha chain	protein	187	2% helix, 40% strand	—
F	C7 TCR beta chain	protein	238	4% helix, 41% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.81	0.83	75	empty
2	986	0.81	0.82	93	empty
3	891	0.78	0.80	71	empty
4	1004	0.77	0.79	97	empty
5	764	0.73	0.78	89	empty

Interfaces

45 interfaces between chains.

I–J · 1842 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 1840 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 1826 Å² buried · 16 hydrogen bonds · protein-protein
O–P · 1734 Å² buried · 10 hydrogen bonds · protein-protein
M–N · 1546 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

5D2L · Crystal structure of TCR C7 in complex with HCMV NLV epitope presented by HLA-A2 · the same entry in another collection · chain R against R, 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 P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5D2L · PDBe 5D2L · UniProt P01892 · UniProt P61769

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