MolNFT v1 · #16777 · protein

Crystal structure of a collagen VIII NC1 domain trimer

1O91 · Collagen alpha 1(VIII) chain: “Crystal structure of a collagen VIII NC1 domain trimer”. X-ray diffraction, 2 ligands (CPS, SO4), 2 pockets (best druggability 0.39). MolNFT v1 #16777 on GenesisL1: 3D structure, binding sites and…

PDB: 1O91
Type: protein
Length: 393 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Collagen alpha 1(VIII) chain
UniProt: Q00780
Ligands: CPS, SO4
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Collagen alpha 1(VIII) chain	protein	131	2% helix, 62% strand	Q00780

Ligands and binding sites

CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · chains B, C
SO4 · Sulfate ion · ion · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.39	0.79	17	empty
2	64	0.35	0.76	9	empty

Interfaces

3 interfaces between chains.

A–C · 1087 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1068 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1035 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1O91 · Crystal Structure of a Collagen VIII NC1 Domain Trimer · the same entry in another collection · chain A against A, TM-score 1.00
Q00780 · AlphaFold monomer V2.0 prediction for collagen alpha-1(VIII) chain (Q00780) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q00780
Elsewhere: RCSB PDB 1O91 · PDBe 1O91 · UniProt Q00780

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