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Crystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody Fab "nabfab"

Analyse Crystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RTH
Type: protein
Length: 4,958 residues
Chains: 27
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fragment antigen-binding light chain; Fragment antigen-binding heavy chain; Nanobody
Ligands: PO4, CL
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 22 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fragment antigen-binding light chain	protein	201	6% helix, 49% strand	—
B	Fragment antigen-binding heavy chain	protein	212	8% helix, 50% strand	—
C	Fragment antigen-binding light chain	protein	204	6% helix, 52% strand	—
D	Fragment antigen-binding heavy chain	protein	228	10% helix, 50% strand	—
E, G	Fragment antigen-binding light chain	protein	209	5% helix, 52% strand	—
F	Fragment antigen-binding heavy chain	protein	225	7% helix, 50% strand	—
H	Fragment antigen-binding heavy chain	protein	225	8% helix, 50% strand	—
I, Q	Fragment antigen-binding light chain	protein	203	6% helix, 52% strand	—
J	Fragment antigen-binding heavy chain	protein	226	10% helix, 50% strand	—
K	Fragment antigen-binding light chain	protein	210	6% helix, 51% strand	—
L	Fragment antigen-binding heavy chain	protein	223	7% helix, 52% strand	—
M	Fragment antigen-binding light chain	protein	207	6% helix, 51% strand	—
N	Fragment antigen-binding heavy chain	protein	221	10% helix, 52% strand	—
O	Fragment antigen-binding light chain	protein	202	3% helix, 53% strand	—
P	Fragment antigen-binding heavy chain	protein	218	9% helix, 51% strand	—
R	Fragment antigen-binding heavy chain	protein	217	10% helix, 53% strand	—
a, c, i	Nanobody	protein	125	7% helix, 47% strand	—
e	Nanobody	protein	124	5% helix, 46% strand	—
g, o	Nanobody	protein	123	5% helix, 45% strand	—
k	Nanobody	protein	126	7% helix, 45% strand	—
m	Nanobody	protein	121	5% helix, 45% strand	—
q	Nanobody	protein	123	5% helix, 46% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 50 copies · chains B, a, C, D, c, E, F, G, I, H, J, i, K, M, L, N, O, Q, R, e, g, m, o, P, q
CL · Chloride ion · ion · 29 copies · chains B, a, C, E, D, c, F, G, H, I, J, K, L, k, M, N, m, O, P, R, Q, e, g, q
GOL · Glycerol · additive · 9 copies · chains B, C, D, E, G, I, L, k, c
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains F, e, H, g, N, m

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.80	0.82	141	PO4, CL
2	991	0.78	0.80	122	PO4, CL
3	383	0.78	0.88	58	CL
4	774	0.75	0.80	90	CL, GOL
5	446	0.74	0.84	62	empty

Interfaces

53 interfaces between chains.

K–L · 2310 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 2210 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 2182 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2179 Å² buried · 20 hydrogen bonds · protein-protein
I–J · 2176 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 45 disulfide (disulfide).

Compared structures

7RTH · Crystal structure of an anti-lysozyme nanobody in complex with an anti-nanobody Fab… · the same entry in another collection · chain B against B, 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 7RTH · PDBe 7RTH

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