SMTL ID : 6cnl.1

Crystal Structure of H105A PGAM5 Dodecamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-12-12-mer

Ligands

31 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: R.38, A.39, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain B: D.134 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: R.52, T.85, R.86 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.5: 8 residues within 4Å: Chain B: A.30, T.31, R.32, R.148, A.149, I.198, R.199, P.200 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.30, B:I.198 MG.6: 5 residues within 4Å: Chain B: R.174, A.175, Q.177 Chain N: W.5, W.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.175 MG.7: 4 residues within 4Å: Chain C: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: R.59, R.96 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain D: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.10: 7 residues within 4Å: Chain D: P.117, D.118, E.181, G.182, W.183, L.184, R.185 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain E: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain E: E.133, D.134, R.137 Chain K: N.144 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.134 MG.13: 3 residues within 4Å: Chain E: M.84, T.85, R.86 No protein-ligand interaction detected (PLIP) MG.14: 6 residues within 4Å: Chain E: S.187, L.188, N.189, G.210 Chain L: R.207, T.208 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain E Metal complexes: L:R.207, E:G.210 MG.15: 4 residues within 4Å: Chain F: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain G: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain H: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain H: R.52, T.85, R.86 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain H: R.169, L.184 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain B: D.107 Chain I: S.105, D.107 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain I: R.38, Y.42, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain F: S.105 Chain J: D.107 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain J: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.25: 5 residues within 4Å: Chain D: R.207 Chain J: S.187, L.188, N.189, G.210 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain J Metal complexes: D:R.207, J:G.210 MG.26: 3 residues within 4Å: Chain E: D.107 Chain K: S.105, D.107 No protein-ligand interaction detected (PLIP) MG.27: 4 residues within 4Å: Chain K: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.28: 7 residues within 4Å: Chain K: P.117, D.118, E.181, G.182, W.183, L.184, R.185 2 PLIP interactions: 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.181, H2O.7 MG.29: 4 residues within 4Å: Chain L: R.52, M.84, T.85, R.86 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain L: R.38, R.86, H.164, A.165 No protein-ligand interaction detected (PLIP) MG.31: 5 residues within 4Å: Chain H: R.174, A.175, Q.177 Chain T: W.5, W.9 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:A.175, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruiz, K. et al., Functional role of PGAM5 multimeric assemblies and their polymerization into filaments. Nat Commun (2019)

Release Date

2019-02-13

Peptides

Serine/threonine-protein phosphatase PGAM5, mitochondrial: ABCDEFGHIJKL
PGAM5 Multimerization Motif Peptide: MNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
L

D
J

E
F

F
H

G
K

H
D

I
B

J
I

K
G

L
E

M
M

N
O

O
X

P
V

Q
R

R
T

S
W

T
P

U
N

V
U

W
S

X
Q

Serine/threonine-protein phosphatase PGAM5, mitochondrial

PGAM5 Multimerization Motif Peptide

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