Research workbench

NIST FAB

Analyse NIST FAB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K8A
Type: protein
Length: 1,744 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Humanized Fab lite chain; Heavy chain
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M, A, E	Humanized Fab lite chain	protein	213	6% helix, 54% strand	—
H, V, B, F	Heavy chain	protein	223	11% helix, 51% strand	—

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.82	0.84	94	empty
2	1019	0.82	0.83	110	empty
3	51	0.67	0.97	16	empty
4	306	0.67	0.82	36	empty
5	435	0.64	0.78	46	empty

Interfaces

17 interfaces between chains.

L–H · 2017 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 2008 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1945 Å² buried · 20 hydrogen bonds · protein-protein
M–V · 1910 Å² buried · 14 hydrogen bonds · protein-protein
H–V · 498 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 4 modified (disulfide, cyclization).

Compared structures

5K8A · NIST FAB · the same entry in another collection · chain L against L, 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 5K8A · PDBe 5K8A

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