Research workbench

Junv GP1 CR1-10 Fab CR1-28 Fab complex

Analyse Junv GP1 CR1-10 Fab CR1-28 Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W1K
Type: protein
Length: 4,045 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CR1-28 Fab light chain; CR1-28 Fab heavy chain; CR1-10 Fab light chain; CR1-10 Fab heavy…
UniProt: P0DOX7, S6C4R2, Q6PIL8, S6B2B6, P26313
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, K, S	CR1-28 Fab light chain	protein	206	7% helix, 44% strand	P0DOX7
B, G, L, T	CR1-28 Fab heavy chain	protein	226	3% helix, 43% strand	S6C4R2
C, H, M	CR1-10 Fab light chain	protein	213	8% helix, 50% strand	Q6PIL8
D, I, O, Q	CR1-10 Fab heavy chain	protein	225	3% helix, 44% strand	S6B2B6
E, P, R	Pre-glycoprotein polyprotein gp complex	protein	142	23% helix, 25% strand	P26313
J	Pre-glycoprotein polyprotein gp complex	protein	141	23% helix, 25% strand	P26313
N	CR1-10 Fab light chain	protein	211	6% helix, 50% strand	Q6PIL8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains E, F, J, K, A, P, R, S, O
BMA · beta-D-mannopyranose · sugar · 3 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.70	0.74	105	empty
2	919	0.68	0.74	83	empty
3	618	0.64	0.75	80	empty
4	318	0.63	0.80	40	empty
5	597	0.63	0.74	71	empty

Interfaces

32 interfaces between chains.

N–O · 2132 Å² buried · 22 hydrogen bonds · protein-protein
H–I · 2076 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 2039 Å² buried · 21 hydrogen bonds · protein-protein
M–Q · 2032 Å² buried · 22 hydrogen bonds · protein-protein
K–L · 1943 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

5W1K · JUNV GP1 CR1-10 Fab CR1-28 Fab complex · the same entry in another collection · chain T against T, 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 P0DOX7
Every structure of UniProt S6C4R2
Every structure of UniProt Q6PIL8
Every structure of UniProt S6B2B6
Every structure of UniProt P26313
Elsewhere: RCSB PDB 5W1K · PDBe 5W1K · UniProt P0DOX7 · UniProt S6C4R2 · UniProt Q6PIL8 · UniProt S6B2B6 · UniProt P26313

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