Research workbench
ACC1 Fab fragment in complex with CII583-591 (CG10)
Analyse ACC1 Fab fragment in complex with CII583-591 (CG10) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MV3
- Type
- protein
- Length
- 3,560 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of ACC1 Fab fragment; Light chain of ACC1 Fab fragment; Synthetic peptide…
- UniProt
- P28481
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 13 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Heavy chain of ACC1 Fab fragment | protein | 216 | 6% helix, 52% strand | — |
| B, J, M, S, V | Light chain of ACC1 Fab fragment | protein | 218 | 6% helix, 53% strand | — |
| X | Synthetic peptide containing the CII583-591 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,SYNTHETIC peptide containing the CII583-591 epitope of collagen type II, | protein | 14 | 0% helix, 0% strand | P28481 |
| C | Heavy chain of ACC1 Fab fragment | protein | 213 | 6% helix, 52% strand | — |
| D, G | Light chain of ACC1 Fab fragment | protein | 217 | 6% helix, 55% strand | — |
| E | Synthetic peptide containing the CII583-591 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,SYNTHETIC peptide containing the CII583-591 epitope of collagen type II, | protein | 13 | 23% helix, 0% strand | P28481 |
| H, Q, T, W | Synthetic peptide containing the CII583-591 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,SYNTHETIC peptide containing the CII583-591 epitope of collagen type II, | protein | 12 | 0% helix, 0% strand | P28481 |
| I, O | Heavy chain of ACC1 Fab fragment | protein | 215 | 6% helix, 50% strand | — |
| K, N | Synthetic peptide containing the CII583-591 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,SYNTHETIC peptide containing the CII583-591 epitope of collagen type II, | protein | 13 | 23% helix, 0% strand | P28481 |
| L | Heavy chain of ACC1 Fab fragment | protein | 220 | 5% helix, 50% strand | — |
| P | Light chain of ACC1 Fab fragment | protein | 215 | 7% helix, 54% strand | — |
| R | Heavy chain of ACC1 Fab fragment | protein | 214 | 6% helix, 53% strand | — |
| U | Heavy chain of ACC1 Fab fragment | protein | 211 | 3% helix, 43% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.81 | 0.85 | 114 | empty |
| 2 | 1042 | 0.76 | 0.78 | 81 | empty |
| 3 | 353 | 0.69 | 0.83 | 41 | empty |
| 4 | 492 | 0.65 | 0.77 | 69 | empty |
| 5 | 217 | 0.63 | 0.83 | 32 | empty |
Interfaces
54 interfaces between chains.
- U–V · 1842 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 1810 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1783 Ų buried · 16 hydrogen bonds · protein-protein
- L–M · 1782 Ų buried · 15 hydrogen bonds · protein-protein
- R–S · 1779 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 9 modified (disulfide, hydroxylation).
Compared structures
- 5MV3 · ACC1 Fab fragment in complex with CII583-591 (CG10) · 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 5MV3 · PDBe 5MV3 · UniProt P28481
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