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Crystal structure of the N. clavipes spidroin ntd at pH 6.5

Analyse Crystal structure of the N. clavipes spidroin ntd at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IZ2
Type: protein
Length: 248 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major ampullate spidroin 1A; Major ampullate spidroin 1A (partial C-terminus)
UniProt: B5SYS5
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Major ampullate spidroin 1A	protein	126	78% helix, 0% strand	B5SYS5
A	Major ampullate spidroin 1A	protein	119	79% helix, 0% strand	B5SYS5
Z	Major ampullate spidroin 1A (partial C-terminus)	protein	3	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	59	0.39	0.80	13	empty

Interfaces

2 interfaces between chains.

B–A · 1230 Å² buried · 9 hydrogen bonds · protein-protein
B–Z · 199 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5IZ2 · Crystal structure of the N. clavipes spidroin NTD at pH 6.5 · the same entry in another collection · chain B against B, 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
Every structure of UniProt B5SYS5
Elsewhere: RCSB PDB 5IZ2 · PDBe 5IZ2 · UniProt B5SYS5

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