MolNFT v1 · #4681 · protein

Idiotopic antibody D1.3 fv fragment-antiidiotopic antibody E5.2 fv fragment complex

1DVF · Fv D1.3: “Idiotopic antibody D1.3 fv fragment-antiidiotopic antibody E5.2 fv fragment complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.75). MolNFT v1 #4681 on GenesisL1: 3D structure, binding sites and…

PDB: 1DVF
Type: protein
Length: 451 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fv D1.3; Fv E5.2
UniProt: P01635, P01820, P01646
Ligands: ZN
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fv D1.3	protein	107	3% helix, 50% strand	P01635
B	Fv D1.3	protein	116	3% helix, 53% strand	P01820
C	Fv E5.2	protein	107	3% helix, 50% strand	P01646
D	Fv E5.2	protein	121	10% helix, 50% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains B, D, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.75	0.90	36	empty
2	101	0.35	0.73	18	empty
3	65	0.28	0.73	17	empty

Interfaces

6 interfaces between chains.

C–D · 1026 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 838 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 577 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 249 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 153 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1DVF · Idiotopic antibody D1.3 fv fragment-antiidiotopic antibody E5.2 fv fragment complex · the same entry in another collection · chain A against A, TM-score 1.00
P01646 · AlphaFold monomer V2.0 prediction for ig kappa chain V-V region hp 123E6 (P01646) · a predicted model of the same protein · chain C against A, TM-score 0.98
P01635 · AlphaFold monomer V2.0 prediction for ig kappa chain V-V region K2 (P01635) · a predicted model of the same protein · chain A against A, TM-score 0.87
P01820 · AlphaFold monomer V2.0 prediction for ig heavy chain V region PJ14 (P01820) · a predicted model of the same protein · chain B against A, TM-score 0.81

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 P01635
Every structure of UniProt P01820
Every structure of UniProt P01646
Elsewhere: RCSB PDB 1DVF · PDBe 1DVF · UniProt P01635 · UniProt P01820 · UniProt P01646

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