MolNFT v1 · #151108 · protein

Crystal structure of apo short afifavidin

6HDS: “Crystal structure of apo short afifavidin”. X-ray diffraction, 3 pockets (best druggability 0.77). MolNFT v1 #151108 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HDS
Type: protein
Length: 492 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short afifavidin
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Short afifavidin	protein	127	6% helix, 61% strand	—
B, C	Short afifavidin	protein	125	6% helix, 62% strand	—
D	Short afifavidin	protein	115	0% helix, 67% strand	—

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	854	0.77	0.80	104	empty
2	86	0.65	0.91	18	empty
3	281	0.55	0.76	29	empty

Interfaces

6 interfaces between chains.

A–C · 1411 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 1383 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 412 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 390 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 129 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6HDS · Crystal Structure of apo short afifavidin · the same entry in another collection · chain D against D, 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 6HDS · PDBe 6HDS

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