Research workbench
Crystal structure of human madcam-1 D1D2 complexed with Fab pf-547659
Analyse Crystal structure of human madcam-1 D1D2 complexed with Fab pf-547659 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HCR
- Type
- protein
- Length
- 1,258 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pf-547659 heavy chain; Pf-547659 light chain; Mucosal addressin cell adhesion molecule 1
- UniProt
- Q13477
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, M | Pf-547659 heavy chain | protein | 217 | 7% helix, 53% strand | — |
| L, N | Pf-547659 light chain | protein | 218 | 6% helix, 51% strand | — |
| A, B | Mucosal addressin cell adhesion molecule 1 | protein | 194 | 2% helix, 57% strand | Q13477 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.77 | 0.80 | 116 | empty |
| 2 | 336 | 0.55 | 0.75 | 40 | empty |
| 3 | 356 | 0.55 | 0.74 | 43 | empty |
| 4 | 56 | 0.47 | 0.85 | 20 | empty |
| 5 | 91 | 0.36 | 0.76 | 27 | empty |
Interfaces
9 interfaces between chains.
- M–N · 1842 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1798 Ų buried · 17 hydrogen bonds · protein-protein
- M–B · 807 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 785 Ų buried · 16 hydrogen bonds · protein-protein
- A–M · 367 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4HCR · Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659 · 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 0.97
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 4HCR · PDBe 4HCR · UniProt Q13477
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