Research workbench

Macv GP1 CR1-07 Fab complex

Analyse Macv GP1 CR1-07 Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W1M
Type: protein
Length: 2,360 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CR1-07 Fab light chain; CR1-07 Fab heavy chain; Pre-glycoprotein polyprotein gp complex
UniProt: Q0KKI6, Q6N089, Q8AZ57
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	CR1-07 Fab light chain	protein	221	6% helix, 51% strand	Q0KKI6
B, F	CR1-07 Fab heavy chain	protein	218	6% helix, 50% strand	Q6N089
D	CR1-07 Fab heavy chain	protein	220	8% helix, 51% strand	Q6N089
G	CR1-07 Fab light chain	protein	219	6% helix, 52% strand	Q0KKI6
H	CR1-07 Fab heavy chain	protein	219	6% helix, 51% strand	Q6N089
Q, S	Pre-glycoprotein polyprotein gp complex	protein	151	23% helix, 22% strand	Q8AZ57
R	Pre-glycoprotein polyprotein gp complex	protein	152	24% helix, 24% strand	Q8AZ57
T	Pre-glycoprotein polyprotein gp complex	protein	149	22% helix, 25% strand	Q8AZ57

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains Q, R, S, T
BMA · beta-D-mannopyranose · sugar · 2 copies

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

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	818	0.76	0.80	102	empty
2	731	0.72	0.78	51	empty
3	215	0.61	0.82	27	empty
4	184	0.59	0.82	27	empty
5	176	0.58	0.82	27	empty

Interfaces

19 interfaces between chains.

C–D · 1838 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 1820 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1793 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1780 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 1160 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 31 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5W1M · MACV GP1 CR1-07 Fab 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 Q0KKI6
Every structure of UniProt Q6N089
Every structure of UniProt Q8AZ57
Elsewhere: RCSB PDB 5W1M · PDBe 5W1M · UniProt Q0KKI6 · UniProt Q6N089 · UniProt Q8AZ57

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