MolNFT v1 · #154925 · protein

Crystal structure of hl homo-diabody

6KR0 · Hl diabody: “Crystal structure of hl homo-diabody”. X-ray diffraction, 10 pockets (best druggability 0.69). MolNFT v1 #154925 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KR0
Type: protein
Length: 906 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hl diabody
Pockets: 10 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hl diabody	protein	228	5% helix, 50% strand	—
B	Hl diabody	protein	228	3% helix, 50% strand	—
C	Hl diabody	protein	227	5% helix, 53% strand	—
D	Hl diabody	protein	223	5% helix, 48% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	847	0.69	0.75	67	empty
2	315	0.58	0.77	42	empty
3	57	0.44	0.83	16	empty
4	108	0.38	0.75	24	empty
5	110	0.36	0.73	26	empty

Interfaces

3 interfaces between chains.

A–B · 1903 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1763 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 198 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6KR0 · Crystal structure of HL homo-diabody · 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 6KR0 · PDBe 6KR0

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