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Crystal structure of the scfv-5E5 in complex with a tn glycopeptide

Analyse Crystal structure of the scfv-5E5 in complex with a tn glycopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TNP
Type: protein
Length: 1,342 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain of our scfv-5E5; Heavy chain of our scfv-5E5
Ligands: NO8
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, J, L	Light chain of our scfv-5E5	protein	112	3% helix, 51% strand	—
B, D, F, H	Heavy chain of our scfv-5E5	protein	115	10% helix, 51% strand	—
I	Heavy chain of our scfv-5E5	protein	109	11% helix, 50% strand	—
K	Heavy chain of our scfv-5E5	protein	101	9% helix, 50% strand	—

Ligands and binding sites

NO8 · (2~{S})-~{N}-[2-[[(2~{S})-1-[[(2~{S},3~{R})-3-[(2~{S}, 3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-1-[[(2~{S})-1-[(2~{S})-2-aminocarbonylpyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-oxidanylidene-ethyl]-1-[(2~{S})-2-azanylpropanoyl]pyrrolidine-2-carboxamide · ligand · 5 copies · chains A, B, L, C, D, E, F, H, G, I

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	979	0.74	0.77	113	empty
2	608	0.72	0.80	69	empty
3	663	0.71	0.78	83	empty
4	1116	0.70	0.75	81	empty
5	416	0.64	0.78	49	NO8

Interfaces

24 interfaces between chains.

E–F · 901 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 898 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 885 Å² buried · 10 hydrogen bonds · protein-protein
H–L · 878 Å² buried · 10 hydrogen bonds · protein-protein
G–I · 867 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6TNP · Crystal structure of the ScFv-5E5 in complex with a Tn glycopeptide · 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 6TNP · PDBe 6TNP

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