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Crystal structure of ntb-a

Analyse Crystal structure of ntb-a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IF7
Type: protein
Length: 757 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Slam family member 6
UniProt: Q96DU3
Ligands: CA, CL
Pockets: 4 · best druggability 0.44

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Slam family member 6	protein	188	6% helix, 53% strand	Q96DU3
B	Slam family member 6	protein	191	4% helix, 51% strand	Q96DU3
C	Slam family member 6	protein	186	4% helix, 43% strand	Q96DU3
D	Slam family member 6	protein	192	6% helix, 49% strand	Q96DU3

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, D
CL · Chloride ion · ion

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

Pockets

4 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	135	0.44	0.77	31	empty
2	90	0.42	0.78	16	empty
3	67	0.30	0.74	15	empty
4	62	0.30	0.75	22	empty

Interfaces

3 interfaces between chains.

C–D · 817 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 769 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 764 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2IF7 · Crystal Structure of NTB-A · the same entry in another collection · chain D against D, TM-score 1.00
Q96DU3 · AlphaFold monomer V2.0 prediction for slam family member 6 (Q96DU3) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 Q96DU3
Elsewhere: RCSB PDB 2IF7 · PDBe 2IF7 · UniProt Q96DU3

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