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Crystal structure of native human madcam-1 D1D2 domain

Analyse Crystal structure of native human madcam-1 D1D2 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HD9
Type: protein
Length: 198 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mucosal addressin cell adhesion molecule 1
UniProt: Q13477
Ligands: NAG
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mucosal addressin cell adhesion molecule 1	protein	198	2% helix, 57% strand	Q13477

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.36	0.78	18	empty

Modifications

Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

4HD9 · Crystal structure of native human MAdCAM-1 D1D2 domain · the same entry in another collection · chain A against A, 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 0.95

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 4HD9 · PDBe 4HD9 · UniProt Q13477

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