MolNFT v1 · #64539 · protein

Crystal structure of the complex between CNTO607 Fab and il-13

3G6D · CNTO607 Fab light chain: “Crystal structure of the complex between CNTO607 Fab and il-13”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.55). MolNFT v1 #64539 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3G6D
Type: protein
Length: 539 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CNTO607 Fab light chain; CNTO607 Fab heavy chain; Interleukin-13
UniProt: P35225
Ligands: SO4
Pockets: 7 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	CNTO607 Fab light chain	protein	210	8% helix, 49% strand	—
H	CNTO607 Fab heavy chain	protein	223	7% helix, 48% strand	—
A	Interleukin-13	protein	106	47% helix, 6% strand	P35225

Ligands and binding sites

SO4 · Sulfate ion · ion · chains H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	420	0.55	0.73	55	empty
2	149	0.46	0.77	26	empty
3	97	0.38	0.76	19	empty
4	107	0.37	0.74	21	empty
5	81	0.32	0.74	24	empty

Interfaces

3 interfaces between chains.

L–H · 1741 Å² buried · 15 hydrogen bonds · protein-protein
L–A · 540 Å² buried · 11 hydrogen bonds · protein-protein
H–A · 476 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3G6D · Crystal structure of the complex between CNTO607 Fab and IL-13 · the same entry in another collection · chain L against L, TM-score 1.00
P35225 · AlphaFold monomer V2.0 prediction for interleukin-13 (P35225) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P35225
Elsewhere: RCSB PDB 3G6D · PDBe 3G6D · UniProt P35225

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