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Crystal structure of npc-biotin-avidin complex

Analyse Crystal structure of npc-biotin-avidin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VHM
Type: protein
Length: 488 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin
UniProt: P02701
Ligands: NPK, NAG, SO4
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Avidin	protein	123	7% helix, 47% strand	P02701
B, D	Avidin	protein	121	7% helix, 49% strand	P02701

Ligands and binding sites

NPK · 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid · ligand · 4 copies · chains A, C, B, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	448	0.71	0.81	50	NPK
2	379	0.70	0.82	41	NPK
3	321	0.70	0.83	40	NPK
4	372	0.69	0.82	46	NPK

Interfaces

6 interfaces between chains.

C–D · 2023 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1926 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 579 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 573 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 155 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3VHM · Crystal structure of NPC-biotin-avidin complex · the same entry in another collection · chain D against D, TM-score 1.00
P02701 · AlphaFold monomer V2.0 prediction for avidin (P02701) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P02701
Elsewhere: RCSB PDB 3VHM · PDBe 3VHM · UniProt P02701

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