MolNFT v1 · #107813 · protein

Induced monomer of the mcg variable domain

4UNT · Ig lambda chain V-II region mgc: “Induced monomer of the mcg variable domain”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.82). MolNFT v1 #107813 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UNT
Type: protein
Length: 864 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig lambda chain V-II region mgc
UniProt: P01709
Ligands: SO4
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G	Ig lambda chain V-II region mgc	protein	109	3% helix, 49% strand	P01709
E	Ig lambda chain V-II region mgc	protein	108	3% helix, 49% strand	P01709
H	Ig lambda chain V-II region mgc	protein	102	0% helix, 43% strand	P01709

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, G, C, F, D, B, E, H

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

Pockets

6 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	1175	0.82	0.83	98	SO4
2	590	0.77	0.83	56	SO4
3	463	0.75	0.84	36	empty
4	129	0.56	0.83	20	empty
5	56	0.32	0.77	20	empty

Interfaces

16 interfaces between chains.

C–E · 1980 Å² buried · 48 hydrogen bonds · protein-protein
A–H · 1964 Å² buried · 51 hydrogen bonds · protein-protein
B–G · 1905 Å² buried · 53 hydrogen bonds · protein-protein
D–F · 1901 Å² buried · 55 hydrogen bonds · protein-protein
C–F · 471 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4UNT · Induced monomer of the Mcg variable domain · the same entry in another collection · chain H against H, TM-score 1.00
P01709 · AlphaFold monomer V2.0 prediction for immunoglobulin lambda variable 2-8 (P01709) · a predicted model of the same protein · chain A against A, TM-score 0.86

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 P01709
Elsewhere: RCSB PDB 4UNT · PDBe 4UNT · UniProt P01709

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