SMTL ID : 8cpr.1

G13D mutant of KRAS4b (2-169) bound to GDP with the switch-I in fully open conformation crystallized in sodium potassium phosphate buffer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 15 residues within 4Å: Chain A: A.12, G.13, D.14, V.15, G.16, K.17, S.18, A.19, N.117, K.118, D.120, L.121, S.146, A.147, K.148 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.12, A:D.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:D.58, A:K.148 Salt bridges: A:K.17, A:D.120 GDP.3: 15 residues within 4Å: Chain B: A.12, G.13, D.14, V.15, G.16, K.17, S.18, A.19, N.117, K.118, D.120, L.121, S.146, A.147, K.148 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.12, B:D.14, B:V.15, B:G.16, B:K.17, B:S.18, B:A.19, B:N.117, B:K.118, B:K.118, B:A.147, B:K.148 Water bridges: B:D.14, B:D.14, B:S.18, B:D.58, B:K.148 Salt bridges: B:K.17, B:D.120

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: A.60, G.61, E.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.61, A:E.64 NA.4: 3 residues within 4Å: Chain B: A.60, G.61, E.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jungholm, O. et al., Novel druggable space in human KRAS G13D discovered using structural bioinformatics and a P-loop targeting monoclonal antibody. Sci Rep (2024)

Release Date

2024-06-12

Peptides

GTPase KRas, N-terminally processed: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GTPase KRas, N-terminally processed

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