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Crystal structure of high-affinity von willebrand factor A1 domain with disulfide mutation in complex with high affinity gpib alpha

Analyse Crystal structure of high-affinity von willebrand factor A1 domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C2B
Type: protein
Length: 1,845 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Von willebrand factor; Platelet glycoprotein ib alpha chain
UniProt: P04275, P07359
Ligands: SO4
Pockets: 19 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 20% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Von willebrand factor	protein	199	36% helix, 21% strand	P04275
B, F	Platelet glycoprotein ib alpha chain	protein	264	8% helix, 22% strand	P07359
C	Von willebrand factor	protein	199	34% helix, 20% strand	P04275
D	Platelet glycoprotein ib alpha chain	protein	262	8% helix, 23% strand	P07359
G	Von willebrand factor	protein	197	35% helix, 22% strand	P04275
H	Platelet glycoprotein ib alpha chain	protein	261	8% helix, 21% strand	P07359

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, H, F, G
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · chains G

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

Pockets

19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.81	0.82	77	empty
2	1104	0.81	0.82	77	empty
3	941	0.80	0.82	73	empty
4	1161	0.79	0.80	76	empty
5	292	0.66	0.82	37	SO4

Interfaces

10 interfaces between chains.

G–H · 1143 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1101 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1089 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 978 Å² buried · 18 hydrogen bonds · protein-protein
B–E · 753 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

P07359 · AlphaFold monomer V2.0 prediction for platelet glycoprotein ib alpha chain (P07359) · a predicted model of the same protein · chain H against A, TM-score 0.98

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 P04275
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Elsewhere: RCSB PDB 4C2B · PDBe 4C2B · UniProt P04275 · UniProt P07359

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