MolNFT v1 · #12501 · protein

Fv mutant Y(B 101)F (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg white lysozyme

1KIQ: “Fv mutant Y(B 101)F (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg white lysozyme”. X-ray diffraction, 2 pockets (best druggability 0.68). MolNFT v1 #12501 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1KIQ
Type: protein
Length: 352 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monoclonal antibody D1.3; Lysozyme
EC: 3.2.1.17
UniProt: P00698
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Monoclonal antibody D1.3	protein	107	3% helix, 50% strand	—
B	Monoclonal antibody D1.3	protein	116	5% helix, 52% strand	—
C	Lysozyme (EC 3.2.1.17)	protein	129	36% helix, 11% strand	P00698

Pockets

2 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	98	0.68	0.92	24	empty
2	91	0.34	0.74	18	empty

Interfaces

3 interfaces between chains.

A–B · 828 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 418 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 361 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1KIQ · Fv mutant Y(B 101)F (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg… · 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
Every structure of UniProt P00698
Elsewhere: RCSB PDB 1KIQ · PDBe 1KIQ · UniProt P00698

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