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Crystal structure of 2F22 Fab fragment against TFPI1

Analyse Crystal structure of 2F22 Fab fragment against TFPI1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NMV
Type: protein
Length: 496 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain; Tissue factor pathway inhibitor
UniProt: P10646
Pockets: 5 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	212	6% helix, 50% strand	—
H	Fab heavy chain	protein	221	8% helix, 51% strand	—
K	Tissue factor pathway inhibitor	protein	63	21% helix, 25% strand	P10646

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains L, H

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	300	0.50	0.73	45	GOL
2	120	0.41	0.76	22	empty
3	93	0.40	0.77	18	empty
4	83	0.39	0.78	20	empty
5	115	0.39	0.75	23	GOL

Interfaces

3 interfaces between chains.

L–H · 1834 Å² buried · 12 hydrogen bonds · protein-protein
H–K · 898 Å² buried · 16 hydrogen bonds · protein-protein
L–K · 448 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5NMV · Crystal structure of 2F22 Fab fragment against TFPI1 · the same entry in another collection · chain K against K, TM-score 1.00
P10646 · AlphaFold monomer V2.0 prediction for tissue factor pathway inhibitor (P10646) · a predicted model of the same protein · chain K against A, TM-score 0.86

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 P10646
Elsewhere: RCSB PDB 5NMV · PDBe 5NMV · UniProt P10646

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