Research workbench

E10 in complex with CXCL13

Analyse E10 in complex with CXCL13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CBE
Type: protein
Length: 601 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E10 heavy chain; E10 light chain; C-X-C motif chemokine 13
UniProt: A0A0B4J2H0, P04209, O43927
Pockets: 8 · best druggability 0.67

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E10 heavy chain	protein	125	2% helix, 54% strand	A0A0B4J2H0
B	E10 light chain	protein	109	3% helix, 48% strand	P04209
C	E10 heavy chain	protein	127	2% helix, 49% strand	A0A0B4J2H0
D	E10 light chain	protein	110	3% helix, 45% strand	P04209
E	C-X-C motif chemokine 13	protein	64	17% helix, 34% strand	O43927
F	C-X-C motif chemokine 13	protein	66	20% helix, 30% strand	O43927

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	132	0.67	0.89	25	empty
2	232	0.54	0.77	37	empty
3	167	0.53	0.79	28	empty
4	159	0.53	0.80	27	empty
5	145	0.45	0.76	30	empty

Interfaces

9 interfaces between chains.

E–F · 973 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 924 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 849 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 817 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 784 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5CBE · E10 in complex with CXCL13 · the same entry in another collection · chain F against F, TM-score 1.00
5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain A against H, TM-score 0.89
5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain A against H, TM-score 0.89
O43927 · AlphaFold monomer V2.0 prediction for C-X-C motif chemokine 13 (O43927) · a predicted model of the same protein · chain E against A, TM-score 0.85

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 A0A0B4J2H0
Every structure of UniProt P04209
Every structure of UniProt O43927
Elsewhere: RCSB PDB 5CBE · PDBe 5CBE · UniProt A0A0B4J2H0 · UniProt P04209 · UniProt O43927

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