MolNFT v1 · #51902 · protein

Structure of anti-collagen type II Fab CIIC1

2VL5 · CIIC1 anticollagen Fab: “Structure of anti-collagen type II Fab CIIC1”. X-ray diffraction, 15 pockets (best druggability 0.62). MolNFT v1 #51902 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VL5
Type: protein
Length: 869 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CIIC1 anticollagen Fab
Pockets: 15 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	CIIC1 anticollagen Fab	protein	218	8% helix, 51% strand	—
B	CIIC1 anticollagen Fab	protein	217	5% helix, 53% strand	—
D	CIIC1 anticollagen Fab	protein	216	6% helix, 53% strand	—

Pockets

15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	560	0.62	0.74	45	empty
2	484	0.60	0.75	64	empty
3	369	0.56	0.74	41	empty
4	84	0.51	0.84	21	empty
5	138	0.45	0.77	20	empty

Interfaces

3 interfaces between chains.

C–D · 1814 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1789 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 239 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2VL5 · Structure of anti-collagen type II FAb CIIC1 · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 2VL5 · PDBe 2VL5

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