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ACC1 Fab fragment in complex with citrullinated C1 epitope of cii (IA03)

Analyse ACC1 Fab fragment in complex with citrullinated C1 epitope of cii (IA03) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MU0
Type: protein
Length: 3,517 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain of ACC1 antibody Fab fragment; Light chain of ACC1 antibody Fab fragment…
UniProt: P28481
Ligands: CIR
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 13 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heavy chain of ACC1 antibody Fab fragment	protein	214	8% helix, 51% strand	—
B, D, H, J, L	Light chain of ACC1 antibody Fab fragment	protein	217	7% helix, 54% strand	—
C, M	Heavy chain of ACC1 antibody Fab fragment	protein	212	8% helix, 52% strand	—
E	Heavy chain of ACC1 antibody Fab fragment	protein	218	8% helix, 50% strand	—
F, P	Light chain of ACC1 antibody Fab fragment	protein	216	7% helix, 55% strand	—
G	Heavy chain of ACC1 antibody Fab fragment	protein	215	8% helix, 51% strand	—
I	Heavy chain of ACC1 antibody Fab fragment	protein	216	8% helix, 51% strand	—
K	Heavy chain of ACC1 antibody Fab fragment	protein	215	8% helix, 51% strand	—
N	Light chain of ACC1 antibody Fab fragment	protein	215	7% helix, 55% strand	—
O	Heavy chain of ACC1 antibody Fab fragment	protein	211	9% helix, 52% strand	—
Q	IA03 peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,IA03 peptide containing the citrullinated C1 epitope of collagen type II	protein	10	0% helix, 0% strand	P28481
R, S, T, U, V, X	IA03 peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,IA03 peptide containing the citrullinated C1 epitope of collagen type II	protein	9	0% helix, 0% strand	P28481
W	IA03 peptide containing the citrullinated C1 epitope of collagen type II,COLLAGEN alpha-1(II) CHAIN,IA03 peptide containing the citrullinated C1 epitope of collagen type II	protein	8	0% helix, 0% strand	P28481

Ligands and binding sites

CIR · Citrulline · ligand · 8 copies · chains A, B, Q, C, D, R, E, F, S, G, H, T, I, J, U, K, L, V, M, N, W, O, P, X

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.80	0.82	131	CIR
2	1041	0.79	0.81	125	CIR
3	856	0.79	0.82	110	empty
4	845	0.79	0.82	93	empty
5	862	0.79	0.82	110	CIR

Interfaces

47 interfaces between chains.

I–J · 1730 Å² buried · 11 hydrogen bonds · protein-protein
K–L · 1729 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1727 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 1698 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1694 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide, 16 covalent, 9 modified (disulfide, covalent ligand, hydroxylation).

Compared structures

5MU0 · ACC1 Fab fragment in complex with citrullinated C1 epitope of CII (IA03) · the same entry in another collection · chain C against C, 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 5MU0 · PDBe 5MU0 · UniProt P28481

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