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Crystal structure of the RP105/MD-1 complex

Analyse Crystal structure of the RP105/MD-1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RG1
Type: protein
Length: 5,669 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD180 molecule; LY86 protein
UniProt: A6QNK7, A4IFT3
Ligands: PGT, MAN, NAG, BMA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 10 distinct chains · 10% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD180 molecule	protein	594	12% helix, 20% strand	A6QNK7
E	CD180 molecule	protein	592	13% helix, 19% strand	A6QNK7
I	CD180 molecule	protein	397	9% helix, 22% strand	A6QNK7
M	CD180 molecule	protein	593	12% helix, 19% strand	A6QNK7
B, F, J, N	CD180 molecule	protein	599	13% helix, 20% strand	A6QNK7
C, G, O	LY86 protein	protein	138	0% helix, 53% strand	A4IFT3
D	LY86 protein	protein	136	0% helix, 53% strand	A4IFT3
H, L	LY86 protein	protein	138	0% helix, 54% strand	A4IFT3
K	LY86 protein	protein	136	0% helix, 52% strand	A4IFT3
P	LY86 protein	protein	135	0% helix, 53% strand	A4IFT3

Ligands and binding sites

PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 4 copies · chains D, H, L, P
MAN · alpha-D-mannopyranose · sugar · 40 copies · chains C, A, G, E, K, I, O, M, D, B, H, F, L, J, P, N
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, C, E, G, I, K, M, O, B, D, F, H, J, L, N, P
BMA · beta-D-mannopyranose · sugar · 16 copies · chains C, G, K, O, D, H, L, P

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

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	956	0.85	0.86	115	empty
2	844	0.84	0.86	91	empty
3	829	0.83	0.86	87	empty
4	708	0.83	0.86	75	empty
5	909	0.82	0.83	72	empty

Interfaces

28 interfaces between chains.

E–G · 1013 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 981 Å² buried · 14 hydrogen bonds · protein-protein
J–L · 962 Å² buried · 12 hydrogen bonds · protein-protein
N–P · 952 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 950 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 66 disulfide, 15 glycan (disulfide, N-glycosylation).

Compared structures

3RG1 · Crystal structure of the RP105/MD-1 complex · the same entry in another collection · chain A against A, 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 A6QNK7
Every structure of UniProt A4IFT3
Elsewhere: RCSB PDB 3RG1 · PDBe 3RG1 · UniProt A6QNK7 · UniProt A4IFT3

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