Research workbench
ACC1 Fab fragment in complex with citrullinated CII616-639 epitope of collagen type II (PTM23)
Analyse ACC1 Fab fragment in complex with citrullinated CII616-639 epitope of collagen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MV4
- Type
- protein
- Length
- 3,565 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACC1 antibody Fab fragment, heavy chain; ACC1 antibody Fab fragment, light chain…
- UniProt
- P28481
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I | ACC1 antibody Fab fragment, heavy chain | protein | 218 | 8% helix, 51% strand | — |
| B, D, M | ACC1 antibody Fab fragment, light chain | protein | 217 | 6% helix, 56% strand | — |
| X, E, N, Q, T, W | Synthetic peptide containing the citrullinated collagen type II epitope CII616-639,COLLAGEN alpha-1(II) CHAIN,SYNTHETIC peptide containing the citrullinated collagen type II epitope CII616- 639 | protein | 12 | 0% helix, 0% strand | P28481 |
| F | ACC1 antibody Fab fragment, heavy chain | protein | 213 | 8% helix, 51% strand | — |
| G, J, P, S, V | ACC1 antibody Fab fragment, light chain | protein | 218 | 6% helix, 56% strand | — |
| H, K | Synthetic peptide containing the citrullinated collagen type II epitope CII616-639,COLLAGEN alpha-1(II) CHAIN,SYNTHETIC peptide containing the citrullinated collagen type II epitope CII616- 639 | protein | 13 | 0% helix, 0% strand | P28481 |
| L | ACC1 antibody Fab fragment, heavy chain | protein | 216 | 8% helix, 51% strand | — |
| O | ACC1 antibody Fab fragment, heavy chain | protein | 216 | 8% helix, 51% strand | — |
| R | ACC1 antibody Fab fragment, heavy chain | protein | 215 | 8% helix, 52% strand | — |
| U | ACC1 antibody Fab fragment, heavy chain | protein | 212 | 8% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, X, C, E, F, H, I, K, L, N, O, Q, R, T, U, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.80 | 0.82 | 109 | empty |
| 2 | 629 | 0.75 | 0.82 | 70 | empty |
| 3 | 1086 | 0.75 | 0.78 | 107 | empty |
| 4 | 475 | 0.69 | 0.80 | 56 | empty |
| 5 | 591 | 0.68 | 0.77 | 61 | empty |
Interfaces
46 interfaces between chains.
- I–J · 1810 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1778 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1778 Ų buried · 16 hydrogen bonds · protein-protein
- O–P · 1762 Ų buried · 13 hydrogen bonds · protein-protein
- U–V · 1761 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 16 modified (disulfide, hydroxylation).
Compared structures
- 5MV4 · ACC1 Fab fragment in complex with citrullinated CII616-639 epitope of collagen type II… · the same entry in another collection · chain H against H, 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 5MV4 · PDBe 5MV4 · UniProt P28481
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