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Crystal structure of an autonomous vh domain

Analyse Crystal structure of an autonomous vh domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3B9V
Type: protein
Length: 471 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain variable domain
Pockets: 7 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Heavy chain variable domain	protein	119	8% helix, 51% strand	—
B	Heavy chain variable domain	protein	116	5% helix, 55% strand	—
D	Heavy chain variable domain	protein	117	8% helix, 55% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	496	0.58	0.74	71	empty
2	107	0.38	0.75	18	empty
3	148	0.38	0.73	26	empty
4	51	0.33	0.78	11	empty
5	65	0.33	0.76	15	empty

Interfaces

4 interfaces between chains.

A–C · 459 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 225 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 224 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 201 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3B9V · Crystal Structure of an Autonomous VH Domain · 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 3B9V · PDBe 3B9V

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