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Crystal structure of a loop deleted mutant of human madcam-1 D1D2 complexed with Fab 10G3

Analyse Crystal structure of a loop deleted mutant of human madcam-1 D1D2 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HC1
Type: protein
Length: 1,262 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucosal addressin cell adhesion molecule 1; 10G3 heavy chain; 10G3 light chain
UniProt: Q13477
Ligands: NAG
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Mucosal addressin cell adhesion molecule 1	protein	198	0% helix, 53% strand	Q13477
H, M	10G3 heavy chain	protein	220	5% helix, 50% strand	—
L, N	10G3 light chain	protein	213	6% helix, 52% strand	—

Ligands and binding sites

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

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

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	748	0.73	0.78	81	empty
2	483	0.63	0.77	48	empty
3	501	0.59	0.74	52	empty
4	468	0.59	0.74	49	empty
5	236	0.56	0.78	28	empty

Interfaces

11 interfaces between chains.

M–N · 1992 Å² buried · 14 hydrogen bonds · protein-protein
H–L · 1944 Å² buried · 12 hydrogen bonds · protein-protein
A–L · 424 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 410 Å² buried · 9 hydrogen bonds · protein-protein
B–N · 408 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4HC1 · Crystal structure of a loop deleted mutant of human MAdCAM-1 D1D2 complexed with Fab 10G3 · the same entry in another collection · chain L against L, TM-score 1.00
Q13477 · AlphaFold monomer V2.0 prediction for mucosal addressin cell adhesion molecule 1 (Q13477) · 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 Q13477
Elsewhere: RCSB PDB 4HC1 · PDBe 4HC1 · UniProt Q13477

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