MolNFT v1 · #127359 · protein
ACC1 Fab fragment in complex with citrullinated C1 epitope of cii (CG05)
5MUB · ACC1 Fab fragment heavy chain: “ACC1 Fab fragment in complex with citrullinated C1 epitope of cii (CG05)”. X-ray diffraction, 2 ligands (CIR, HYP), 20 pockets (best druggability 0.80). MolNFT v1 #127359 on GenesisL1: 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
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