MolNFT v1 · #102745 · protein

Structure of HLA-DR1 with a bound peptide with non-optimal alanine in the P1 pocket

4OV5 · HLA class II histocompatibility antigen, dr alpha chain: “Structure of HLA-DR1 with a bound peptide with non-optimal alanine in the P1 pocket”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #102745 on GenesisL1…

PDB: 4OV5
Type: protein
Length: 2,279 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
UniProt: P01903, P04229, P01892
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 10 distinct chains · 16% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	180	14% helix, 47% strand	P01903
B, H, Q	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	189	17% helix, 46% strand	P04229
D, G	HLA class II histocompatibility antigen, dr alpha chain	protein	179	15% helix, 46% strand	P01903
E	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	186	19% helix, 46% strand	P04229
J	HLA class II histocompatibility antigen, dr alpha chain	protein	177	15% helix, 47% strand	P01903
K	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	187	18% helix, 47% strand	P04229
M, P	HLA class II histocompatibility antigen, dr alpha chain	protein	179	14% helix, 47% strand	P01903
N	HLA class II histocompatibility antigen, DRB1-1 beta chain	protein	185	18% helix, 46% strand	P04229
C, F, L, O, R	HLA class I histocompatibility antigen, a-2 alpha chain	protein	14	0% helix, 7% strand	P01892
I	HLA class I histocompatibility antigen, a-2 alpha chain	protein	11	0% helix, 9% strand	P01892

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.75	0.78	92	empty
2	1067	0.73	0.76	126	empty
3	1145	0.73	0.76	99	empty
4	670	0.67	0.76	58	empty
5	558	0.66	0.77	51	empty

Interfaces

38 interfaces between chains.

A–B · 2566 Å² buried · 43 hydrogen bonds · protein-protein
D–E · 2523 Å² buried · 42 hydrogen bonds · protein-protein
G–H · 2494 Å² buried · 42 hydrogen bonds · protein-protein
J–K · 2466 Å² buried · 41 hydrogen bonds · protein-protein
M–N · 2466 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

4OV5 · Structure of HLA-DR1 with a bound peptide with non-optimal alanine in the P1 pocket · 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 P01903
Every structure of UniProt P04229
Every structure of UniProt P01892
Elsewhere: RCSB PDB 4OV5 · PDBe 4OV5 · UniProt P01903 · UniProt P04229 · UniProt P01892

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