Research workbench

Crystal structure of complement C4B re-refined using imdff

Analyse Crystal structure of complement C4B re-refined using imdff in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JTW
Type: protein
Length: 3,128 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C4-a
UniProt: P0C0L4
Ligands: NAG
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Complement C4-a	protein	651	8% helix, 49% strand	P0C0L4
B, E	Complement C4-a	protein	632	33% helix, 28% strand	P0C0L4
C, F	Complement C4-a	protein	281	13% helix, 38% strand	P0C0L4

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, E

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	811	0.72	0.78	54	empty
2	665	0.71	0.78	70	empty
3	779	0.71	0.77	63	empty
4	333	0.70	0.83	60	empty
5	305	0.62	0.79	31	empty

Interfaces

9 interfaces between chains.

A–B · 5237 Å² buried · 100 hydrogen bonds · protein-protein
D–E · 5219 Å² buried · 92 hydrogen bonds · protein-protein
E–F · 2631 Å² buried · 40 hydrogen bonds · protein-protein
B–C · 2613 Å² buried · 38 hydrogen bonds · protein-protein
D–F · 864 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5JTW · Crystal structure of complement C4b re-refined using iMDFF · the same entry in another collection · chain F against F, TM-score 1.00
P0C0L4 · AlphaFold monomer V2.0 prediction for complement C4-a (P0C0L4) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P0C0L4
Elsewhere: RCSB PDB 5JTW · PDBe 5JTW · UniProt P0C0L4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.