8T09: Krev interaction trapped protein 1

Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative (6-ethynyl-2-hydroxy-1-naphthaldehyde). Determined by X-ray diffraction at 2.15 Å resolution. Released 13 Dec 2023.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,929
Mol. weight: 56.78 kDa
Ligands: XHZ, MG, GNP
Released: 13 Dec 2023

Explore 8T09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T09 contains 23 α-helices and 20 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	421-425	5	1
β-strand	431-435	5	1
α-helix	439-441	3
α-helix	444-449	6
α-helix	455-458	4
β-strand	461-466	6	1
β-strand	471-473	3	1
α-helix	474-475	2
α-helix	480-485	6
α-helix	487-494	8
α-helix	499-501	3
β-strand	505-510	6	1
α-helix	516-519	4
α-helix	525-541	17
α-helix	548-563	16
α-helix	568-571	4
α-helix	578-582	5
α-helix	587-590	4
α-helix	594-597	4
α-helix	598-610	13
α-helix	618-630	13
β-strand	638-646	9	2
β-strand	654-662	9	2
β-strand	666-671	6	2
β-strand	677-682	6	2
β-strand	686-690	5	2
β-strand	696-701	6	2
β-strand	706-711	6	2
α-helix	715-728	14

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	37-45	9	1
β-strand	50-58	9	1
α-helix	68-74	7
β-strand	77-83	7	1
α-helix	87-104	18
β-strand	111-116	6	1
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	1
β-strand	147	1	3
β-strand	152	1	3
α-helix	155-166	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Krev interaction trapped protein 1	A	protein	318	Homo sapiens	O00522 (AlphaFold model)
Ras-related protein Rap-1b	B	protein	167	Homo sapiens	P61224 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8T09_1 Krev interaction trapped protein 1 (chains A)
YEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQLKPYH
KPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDEARYN
LLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKAPHWT
NRILHEYKNLSTSEGVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFTKASPSNHKVIPV
YVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQAGLV
VKLLMKLNGQLMPTERNS

Sequence of entity 2 (B), FASTA

>8T09_2 Ras-related protein Rap-1b (chains B)
MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAG
TEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDL
EDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

Ligands and cofactors

ID	Name	Formula	Copies
XHZ	6-ethynyl-2-hydroxynaphthalene-1-carbaldehyde	C13 H8 O2	1
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Primary citation

Targeted Reversible Covalent Modification of a Noncatalytic Lysine of the Krev Interaction Trapped 1 Protein Enables Site-Directed Screening for Protein-Protein Interaction Inhibitors. Francisco, K.R., Bruystens, J., Varricchio, C. et al. Acs Pharmacol Transl Sci (2023) 6:1651-1658. DOI 10.1021/acsptsci.3c00156 · PubMed

Other PDB entries of the same protein (UniProt O00522 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HDO 1.67 Å, Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase
4JIF 1.7 Å, Co-crystal structure of ICAP1 PTB domain in complex with a KRIT1 peptide
6OQ4 1.75 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi1
6OQ3 1.85 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2
6UZK 1.92 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6
4DXA 1.95 Å, Co-crystal structure of Rap1 in complex with KRIT1
4HDQ 1.95 Å, Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and the…
8SU8 2.01 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
8T7V 2.25 Å, Co-crystal structure of KRIT1 with a 1-hydroxy 2-naphthaldehyde derivative…
3U7D 2.49 Å, Crystal structure of the KRIT1/CCM1 FERM domain in complex with the heart of glass…
4DX8 2.54 Å, ICAP1 in complex with KRIT1 N-terminus
5D68 2.91 Å, Crystal structure of KRIT1 ARD-FERM

Browse structure collections

About this viewer

MolViewer shows 8T09 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.