SMTL ID : 9lgo.1

Cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.51 Å

Oligo State

hetero-4-2-2-2-mer

Ligands

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 11 residues within 4Å: Chain A: M.354, G.356, G.397, T.398, G.399, K.400, T.401, M.402, N.500, G.561, K.565 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.356, A:G.356, A:G.397, A:T.398, A:G.399, A:T.401, A:T.401, A:M.402, A:N.500, A:N.500 Salt bridges: A:K.400, A:K.400 ATP.2: 14 residues within 4Å: Chain A: R.784 Chain F: E.465, G.467, G.508, C.509, A.510, K.511, T.512, T.513, E.565, I.661, G.689, A.690, R.693 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain F Salt bridges: A:R.784, F:K.511 Hydrogen bonds: F:G.467, F:G.467, F:G.508, F:C.509, F:A.510, F:K.511, F:T.512, F:T.512, F:T.513, F:T.513, F:E.565 ATP.3: 14 residues within 4Å: Chain A: R.511 Chain F: L.202, G.203, P.243, G.244, V.245, G.246, K.247, T.248, Q.249, E.304, N.345, G.405, T.409 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.203, F:G.244, F:V.245, F:G.246, F:K.247, F:T.248, F:Q.249, F:E.304, F:N.345, F:T.409 Salt bridges: F:K.247, F:K.247, A:R.511 ATP.4: 7 residues within 4Å: Chain G: P.396, G.397, K.400, T.401, M.402, A.562, K.565 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.397 Salt bridges: G:K.400, G:K.400 ATP.5: 12 residues within 4Å: Chain H: G.356, P.396, G.397, T.398, G.399, K.400, T.401, M.402, N.500, G.561, A.562, K.565 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:G.356, H:G.356, H:G.397, H:T.398, H:G.399, H:K.400, H:T.401, H:T.401, H:M.402, H:Q.454, H:N.500 Salt bridges: H:K.400, H:K.400 ATP.6: 17 residues within 4Å: Chain H: R.784 Chain I: E.465, I.466, G.467, P.507, G.508, C.509, A.510, K.511, T.512, T.513, D.564, E.565, N.629, I.661, G.689, R.693 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:G.467, I:G.467, I:G.508, I:A.510, I:K.511, I:T.512, I:T.512, I:T.513, I:T.513, I:E.565, I:E.565, I:N.629 Salt bridges: I:K.511, H:R.784 ATP.7: 14 residues within 4Å: Chain I: P.201, G.203, P.243, G.244, V.245, G.246, K.247, T.248, Q.249, N.345, I.377, G.405, T.409 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:G.203, I:G.203, I:G.244, I:V.245, I:G.246, I:K.247, I:T.248, I:Q.249, I:Q.249, I:N.345 Salt bridges: I:K.247, I:K.247 ATP.9: 11 residues within 4Å: Chain J: I.355, G.397, T.398, G.399, K.400, T.401, M.402, I.532, G.561, A.562, K.565 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:G.397, J:K.400, J:T.401, J:T.401 Salt bridges: J:K.400, J:K.400

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain I: T.248, D.303 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, Y. et al., cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex. To Be Published

Release Date

2025-04-23

Peptides

ATPase family gene 2 protein homolog A: AGHJ
Cyclin-dependent kinase 2-interacting protein: BC
cDNA FLJ55172: DE
ATPase family gene 2 protein homolog B: FI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

H
D

J
B

B
J

C
I

D
H

E
G

F
F

I
C

ATPase family gene 2 protein homolog A

Cyclin-dependent kinase 2-interacting protein

cDNA FLJ55172

ATPase family gene 2 protein homolog B