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Rhodocetin in complex with the integrin ALPHA2-a domain

Analyse Rhodocetin in complex with the integrin ALPHA2-a domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5THP
Type: protein
Length: 2,640 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Snaclec rhodocetin subunit gamma; Snaclec rhodocetin subunit delta; Integrin alpha-2
UniProt: D2YW39, D2YW40, P17301
Ligands: NA, MG, CL, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 14 distinct chains · 29% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Snaclec rhodocetin subunit gamma	protein	129	16% helix, 22% strand	D2YW39
B	Snaclec rhodocetin subunit delta	protein	119	15% helix, 30% strand	D2YW40
C	Integrin alpha-2	protein	190	40% helix, 15% strand	P17301
D	Snaclec rhodocetin subunit gamma	protein	130	19% helix, 26% strand	D2YW39
E, N, Q	Snaclec rhodocetin subunit delta	protein	122	17% helix, 34% strand	D2YW40
F	Integrin alpha-2	protein	193	39% helix, 18% strand	P17301
G, M, P	Snaclec rhodocetin subunit gamma	protein	132	17% helix, 30% strand	D2YW39
H	Snaclec rhodocetin subunit delta	protein	120	17% helix, 28% strand	D2YW40
I	Integrin alpha-2	protein	191	38% helix, 17% strand	P17301
J	Snaclec rhodocetin subunit gamma	protein	131	18% helix, 27% strand	D2YW39
K	Snaclec rhodocetin subunit delta	protein	108	12% helix, 31% strand	D2YW40
L	Integrin alpha-2	protein	189	39% helix, 14% strand	P17301
O	Integrin alpha-2	protein	191	41% helix, 19% strand	P17301
R	Integrin alpha-2	protein	187	38% helix, 18% strand	P17301

Ligands and binding sites

NA · Sodium ion · metal · 31 copies · chains A, B, C, O, D, J, E, F, G, H, I, K, L, M, N, P, Q, R
MG · Magnesium ion · metal · 6 copies · chains C, F, I, L, O, R
CL · Chloride ion · ion · 35 copies · chains A, I, C, O, D, E, J, F, G, H, L, K, M, N, R, P, Q
SO4 · Sulfate ion · ion · 10 copies · chains B, C, D, E, F, H, I, K, L, N, O, Q, R
GOL · Glycerol · additive · 8 copies · chains A, I, C, G, H, J, K, P, Q, R

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1068	0.83	0.84	127	CL, GOL, SO4
2	945	0.80	0.82	112	GOL, NA
3	827	0.76	0.80	61	MG, CL, SO4
4	650	0.75	0.82	60	CL, NA, SO4
5	697	0.74	0.80	53	CL, GOL, SO4

Interfaces

31 interfaces between chains.

M–N · 2015 Å² buried · 31 hydrogen bonds · protein-protein
G–H · 1996 Å² buried · 30 hydrogen bonds · protein-protein
P–Q · 1895 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1879 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1876 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 disulfide (disulfide).

Compared structures

5THP · Rhodocetin in complex with the integrin alpha2-A domain · the same entry in another collection · chain K against K, 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 D2YW39
Every structure of UniProt D2YW40
Every structure of UniProt P17301
Elsewhere: RCSB PDB 5THP · PDBe 5THP · UniProt D2YW39 · UniProt D2YW40 · UniProt P17301

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