MolNFT v1 · #122278 · protein

X-ray structure of the N-terminal domain of human doublecortin in complex with Fab

5IKC · Mab 6H10 light chain: “X-ray structure of the N-terminal domain of human doublecortin in complex with Fab”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.75). MolNFT v1 #122278 on GenesisL1: 3D structure, binding…

PDB: 5IKC
Type: protein
Length: 1,029 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mab 6H10 light chain; Ighg protein; Neuronal migration protein doublecortin
UniProt: A0A0U5BC76, Q569X1, O43602
Ligands: CL
Pockets: 15 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mab 6H10 light chain	protein	213	5% helix, 53% strand	A0A0U5BC76
B	Ighg protein	protein	211	6% helix, 54% strand	Q569X1
H	Ighg protein	protein	215	8% helix, 53% strand	Q569X1
L	Mab 6H10 light chain	protein	211	6% helix, 50% strand	A0A0U5BC76
M	Neuronal migration protein doublecortin	protein	89	17% helix, 25% strand	O43602
N	Neuronal migration protein doublecortin	protein	90	16% helix, 24% strand	O43602

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains B, M, H, N

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

Pockets

15 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	478	0.75	0.84	51	empty
2	283	0.67	0.83	31	empty
3	475	0.59	0.74	47	empty
4	169	0.51	0.78	35	empty
5	81	0.48	0.82	19	empty

Interfaces

10 interfaces between chains.

H–L · 1850 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1760 Å² buried · 15 hydrogen bonds · protein-protein
B–M · 629 Å² buried · 16 hydrogen bonds · protein-protein
H–N · 622 Å² buried · 16 hydrogen bonds · protein-protein
B–H · 490 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).

Compared structures

5IKC · X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB · the same entry in another collection · chain N against N, TM-score 1.00
O43602 · AlphaFold monomer V2.0 prediction for neuronal migration protein doublecortin (O43602) · a predicted model of the same protein · chain M 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 A0A0U5BC76
Every structure of UniProt Q569X1
Every structure of UniProt O43602
Elsewhere: RCSB PDB 5IKC · PDBe 5IKC · UniProt A0A0U5BC76 · UniProt Q569X1 · UniProt O43602

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