Research workbench
ACC1 Fab fragment in complex with citrullinated C1 epitope of cii (CG05)
Analyse ACC1 Fab fragment in complex with citrullinated C1 epitope of cii (CG05) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MUB
- Type
- protein
- Length
- 3,531 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACC1 Fab fragment heavy chain; ACC1 Fab fragment light chain; Triple-helical peptide…
- UniProt
- P28481
- Ligands
- CIR, HYP
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 14 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ACC1 Fab fragment heavy chain | protein | 217 | 8% helix, 52% strand | — |
| B, D, G, J, M, P, S, V | ACC1 Fab fragment light chain | protein | 217 | 6% helix, 53% strand | — |
| X | Triple-helical peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,TRIPLE-helical peptide containing the citrullinated C1 epitope of collagen type II | protein | 9 | 0% helix, 0% strand | P28481 |
| C | ACC1 Fab fragment heavy chain | protein | 216 | 8% helix, 52% strand | — |
| E, H, N, W | Triple-helical peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,TRIPLE-helical peptide containing the citrullinated C1 epitope of collagen type II | protein | 7 | 0% helix, 0% strand | P28481 |
| F | ACC1 Fab fragment heavy chain | protein | 217 | 8% helix, 52% strand | — |
| I | ACC1 Fab fragment heavy chain | protein | 217 | 8% helix, 52% strand | — |
| K | Triple-helical peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,TRIPLE-helical peptide containing the citrullinated C1 epitope of collagen type II | protein | 9 | 0% helix, 0% strand | P28481 |
| L | ACC1 Fab fragment heavy chain | protein | 216 | 8% helix, 52% strand | — |
| O | ACC1 Fab fragment heavy chain | protein | 212 | 8% helix, 53% strand | — |
| Q | Triple-helical peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,TRIPLE-helical peptide containing the citrullinated C1 epitope of collagen type II | protein | 6 | 0% helix, 0% strand | P28481 |
| R | ACC1 Fab fragment heavy chain | protein | 220 | 8% helix, 51% strand | — |
| T | Triple-helical peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,TRIPLE-helical peptide containing the citrullinated C1 epitope of collagen type II | protein | 10 | 0% helix, 0% strand | P28481 |
| U | ACC1 Fab fragment heavy chain | protein | 218 | 8% helix, 51% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · 8 copies · chains A, B, X, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W
- HYP · 4-hydroxyproline · ligand · 7 copies · chains B, X, D, E, G, H, M, N, P, Q, S, T, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.80 | 0.82 | 106 | empty |
| 2 | 651 | 0.79 | 0.84 | 76 | empty |
| 3 | 900 | 0.79 | 0.81 | 102 | empty |
| 4 | 565 | 0.78 | 0.85 | 72 | empty |
| 5 | 698 | 0.78 | 0.83 | 82 | empty |
Interfaces
53 interfaces between chains.
- R–S · 1760 Ų buried · 17 hydrogen bonds · protein-protein
- U–V · 1746 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1730 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1725 Ų buried · 16 hydrogen bonds · protein-protein
- L–M · 1714 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 9 covalent, 3 modified (disulfide, covalent ligand, hydroxylation).
Compared structures
- 5MUB · ACC1 Fab fragment in complex with citrullinated C1 epitope of CII (CG05) · the same entry in another collection · chain J against J, TM-score 1.00
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 P28481
- Elsewhere: RCSB PDB 5MUB · PDBe 5MUB · UniProt P28481
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.