MolNFT v1 · #137283 · protein

Complex between HYHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and pekin duck egg lysozyme isoform I (del-I)

5VJQ · HYHEL10 heavy chain Fab fragment carrying three mutations: “Complex between HYHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and pekin duck egg lysozyme…”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability…

PDB: 5VJQ
Type: protein
Length: 2,186 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HYHEL10 heavy chain Fab fragment carrying three mutations; HYHEL10 light chain Fab…
EC: 3.2.1.18
UniProt: U3J0P1
Ligands: CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 17% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HYHEL10 heavy chain Fab fragment carrying three mutations (EC 3.2.1.18)	protein	208	9% helix, 51% strand	—
B, F, H	HYHEL10 light chain Fab fragment	protein	212	6% helix, 51% strand	—
I, J	Lysozyme	protein	129	41% helix, 11% strand	U3J0P1
C, E	HYHEL10 heavy chain Fab fragment carrying three mutations (EC 3.2.1.18)	protein	207	9% helix, 52% strand	—
D	HYHEL10 light chain Fab fragment	protein	213	6% helix, 50% strand	—
K	Lysozyme	protein	125	43% helix, 11% strand	U3J0P1
G	HYHEL10 heavy chain Fab fragment carrying three mutations (EC 3.2.1.18)	protein	206	9% helix, 52% strand	—
L	Lysozyme	protein	126	41% helix, 11% strand	U3J0P1

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B, I, C, D, J, E, F, K, G, H, L
GOL · Glycerol · additive · 6 copies · chains C, J, D, E, K, G, H

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	891	0.82	0.84	109	empty
2	752	0.77	0.81	98	empty
3	647	0.73	0.80	78	empty
4	998	0.71	0.75	92	empty
5	253	0.65	0.82	31	empty

Interfaces

26 interfaces between chains.

A–B · 1792 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1756 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1680 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1644 Å² buried · 12 hydrogen bonds · protein-protein
A–I · 553 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

5VJQ · Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin duck… · 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 U3J0P1
Elsewhere: RCSB PDB 5VJQ · PDBe 5VJQ · UniProt U3J0P1

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