SMTL ID : 7oj5.1

Cryo-EM structure of Medicago truncatula HISN5 protein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

48 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.73, E.77, H.145 Chain J: H.170 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: A:H.73, A:E.77, A:H.145, J:H.170, H2O.14 MN.2: 4 residues within 4Å: Chain A: H.47, H.169, E.173 Chain V: H.74 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain V Metal complexes: A:H.47, A:H.169, A:E.173, A:E.173, V:H.74 MN.3: 4 residues within 4Å: Chain B: H.73, E.77, H.145 Chain I: H.170 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: B:H.73, B:E.77, B:H.145, I:H.170, H2O.13 MN.4: 4 residues within 4Å: Chain B: H.47, H.169, E.173 Chain N: H.74 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain N Metal complexes: B:H.47, B:H.169, B:E.173, B:E.173, N:H.74 MN.5: 4 residues within 4Å: Chain C: H.73, E.77, H.145 Chain F: H.170 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: C:H.73, C:E.77, C:H.145, F:H.170, H2O.8 MN.6: 4 residues within 4Å: Chain C: H.47, H.169, E.173 Chain Q: H.74 5 PLIP interactions: 1 interactions with chain Q, 4 interactions with chain C Metal complexes: Q:H.74, C:H.47, C:H.169, C:E.173, C:E.173 MN.7: 4 residues within 4Å: Chain D: H.73, E.77, H.145 Chain S: H.170 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain S, 1 Ligand-Water interactions Metal complexes: D:H.73, D:E.77, D:H.145, S:H.170, H2O.28 MN.8: 4 residues within 4Å: Chain D: H.47, H.169, E.173 Chain H: H.74 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain H Metal complexes: D:H.47, D:H.169, D:E.173, D:E.173, H:H.74 MN.9: 4 residues within 4Å: Chain E: H.73, E.77, H.145 Chain L: H.170 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: E:H.73, E:E.77, E:H.145, L:H.170, H2O.17 MN.10: 4 residues within 4Å: Chain E: H.47, H.169, E.173 Chain X: H.74 5 PLIP interactions: 1 interactions with chain X, 4 interactions with chain E Metal complexes: X:H.74, E:H.47, E:H.169, E:E.173, E:E.173 MN.11: 4 residues within 4Å: Chain F: H.73, E.77, H.145 Chain T: H.170 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain T, 1 Ligand-Water interactions Metal complexes: F:H.73, F:E.77, F:H.145, T:H.170, H2O.29 MN.12: 4 residues within 4Å: Chain C: H.74 Chain F: H.47, H.169, E.173 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain C Metal complexes: F:H.47, F:H.169, F:E.173, F:E.173, C:H.74 MN.13: 4 residues within 4Å: Chain G: H.73, E.77, H.145 Chain W: H.170 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: G:H.73, G:E.77, G:H.145, W:H.170, H2O.34 MN.14: 4 residues within 4Å: Chain G: H.47, H.169, E.173 Chain M: H.74 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain M Metal complexes: G:H.47, G:H.169, G:E.173, G:E.173, M:H.74 MN.15: 4 residues within 4Å: Chain D: H.170 Chain H: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: H:H.73, H:E.77, H:H.145, D:H.170, H2O.5 MN.16: 4 residues within 4Å: Chain H: H.47, H.169, E.173 Chain O: H.74 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain O Metal complexes: H:H.47, H:H.169, H:E.173, H:E.173, O:H.74 MN.17: 4 residues within 4Å: Chain I: H.73, E.77, H.145 Chain U: H.170 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain U, 1 Ligand-Water interactions Metal complexes: I:H.73, I:E.77, I:H.145, U:H.170, H2O.31 MN.18: 4 residues within 4Å: Chain B: H.74 Chain I: H.47, H.169, E.173 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain B Metal complexes: I:H.47, I:H.169, I:E.173, I:E.173, B:H.74 MN.19: 4 residues within 4Å: Chain J: H.73, E.77, H.145 Chain R: H.170 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain R, 1 Ligand-Water interactions Metal complexes: J:H.73, J:E.77, J:H.145, R:H.170, H2O.26 MN.20: 4 residues within 4Å: Chain A: H.74 Chain J: H.47, H.169, E.173 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain A Metal complexes: J:H.47, J:H.169, J:E.173, J:E.173, A:H.74 MN.21: 4 residues within 4Å: Chain K: H.73, E.77, H.145 Chain X: H.170 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain X, 1 Ligand-Water interactions Metal complexes: K:H.73, K:E.77, K:H.145, X:H.170, H2O.35 MN.22: 4 residues within 4Å: Chain K: H.47, H.169, E.173 Chain L: H.74 5 PLIP interactions: 1 interactions with chain L, 4 interactions with chain K Metal complexes: L:H.74, K:H.47, K:H.169, K:E.173, K:E.173 MN.23: 4 residues within 4Å: Chain K: H.170 Chain L: H.73, E.77, H.145 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:H.170, L:H.73, L:E.77, L:H.145, H2O.16 MN.24: 4 residues within 4Å: Chain E: H.74 Chain L: H.47, H.169, E.173 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain E Metal complexes: L:H.47, L:H.169, L:E.173, L:E.173, E:H.74 MN.25: 4 residues within 4Å: Chain G: H.170 Chain M: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain M, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: M:H.73, M:E.77, M:H.145, G:H.170, H2O.10 MN.26: 4 residues within 4Å: Chain M: H.47, H.169, E.173 Chain P: H.74 5 PLIP interactions: 1 interactions with chain P, 4 interactions with chain M Metal complexes: P:H.74, M:H.47, M:H.169, M:E.173, M:E.173 MN.27: 4 residues within 4Å: Chain B: H.170 Chain N: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain N, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: N:H.73, N:E.77, N:H.145, B:H.170, H2O.2 MN.28: 4 residues within 4Å: Chain N: H.47, H.169, E.173 Chain U: H.74 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain U Metal complexes: N:H.47, N:H.169, N:E.173, N:E.173, U:H.74 MN.29: 4 residues within 4Å: Chain H: H.170 Chain O: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain O, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: O:H.73, O:E.77, O:H.145, H:H.170, H2O.11 MN.30: 4 residues within 4Å: Chain O: H.47, H.169, E.173 Chain S: H.74 5 PLIP interactions: 1 interactions with chain S, 4 interactions with chain O Metal complexes: S:H.74, O:H.47, O:H.169, O:E.173, O:E.173 MN.31: 4 residues within 4Å: Chain M: H.170 Chain P: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain P, 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: P:H.73, P:E.77, P:H.145, M:H.170, H2O.19 MN.32: 4 residues within 4Å: Chain P: H.47, H.169, E.173 Chain W: H.74 5 PLIP interactions: 4 interactions with chain P, 1 interactions with chain W Metal complexes: P:H.47, P:H.169, P:E.173, P:E.173, W:H.74 MN.33: 4 residues within 4Å: Chain C: H.170 Chain Q: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: Q:H.73, Q:E.77, Q:H.145, C:H.170, H2O.4 MN.34: 4 residues within 4Å: Chain Q: H.47, H.169, E.173 Chain T: H.74 5 PLIP interactions: 4 interactions with chain Q, 1 interactions with chain T Metal complexes: Q:H.47, Q:H.169, Q:E.173, Q:E.173, T:H.74 MN.35: 4 residues within 4Å: Chain R: H.73, E.77, H.145 Chain V: H.170 5 PLIP interactions: 1 interactions with chain V, 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: V:H.170, R:H.73, R:E.77, R:H.145, H2O.32 MN.36: 4 residues within 4Å: Chain J: H.74 Chain R: H.47, H.169, E.173 5 PLIP interactions: 1 interactions with chain J, 4 interactions with chain R Metal complexes: J:H.74, R:H.47, R:H.169, R:E.173, R:E.173 MN.37: 4 residues within 4Å: Chain O: H.170 Chain S: H.73, E.77, H.145 5 PLIP interactions: 1 interactions with chain O, 3 interactions with chain S, 1 Ligand-Water interactions Metal complexes: O:H.170, S:H.73, S:E.77, S:H.145, H2O.22 MN.38: 4 residues within 4Å: Chain D: H.74 Chain S: H.47, H.169, E.173 5 PLIP interactions: 4 interactions with chain S, 1 interactions with chain D Metal complexes: S:H.47, S:H.169, S:E.173, S:E.173, D:H.74 MN.39: 4 residues within 4Å: Chain Q: H.170 Chain T: H.73, E.77, H.145 5 PLIP interactions: 1 interactions with chain Q, 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: Q:H.170, T:H.73, T:E.77, T:H.145, H2O.25 MN.40: 4 residues within 4Å: Chain F: H.74 Chain T: H.47, H.169, E.173 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain T Metal complexes: F:H.74, T:H.47, T:H.169, T:E.173, T:E.173 MN.41: 4 residues within 4Å: Chain N: H.170 Chain U: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain U, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: U:H.73, U:E.77, U:H.145, N:H.170, H2O.20 MN.42: 4 residues within 4Å: Chain I: H.74 Chain U: H.47, H.169, E.173 5 PLIP interactions: 1 interactions with chain I, 4 interactions with chain U Metal complexes: I:H.74, U:H.47, U:H.169, U:E.173, U:E.173 MN.43: 4 residues within 4Å: Chain A: H.170 Chain V: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain V, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: V:H.73, V:E.77, V:H.145, A:H.170, H2O.1 MN.44: 4 residues within 4Å: Chain R: H.74 Chain V: H.47, H.169, E.173 5 PLIP interactions: 4 interactions with chain V, 1 interactions with chain R Metal complexes: V:H.47, V:H.169, V:E.173, V:E.173, R:H.74 MN.45: 4 residues within 4Å: Chain P: H.170 Chain W: H.73, E.77, H.145 5 PLIP interactions: 1 interactions with chain P, 3 interactions with chain W, 1 Ligand-Water interactions Metal complexes: P:H.170, W:H.73, W:E.77, W:H.145, H2O.23 MN.46: 4 residues within 4Å: Chain G: H.74 Chain W: H.47, H.169, E.173 5 PLIP interactions: 1 interactions with chain G, 4 interactions with chain W Metal complexes: G:H.74, W:H.47, W:H.169, W:E.173, W:E.173 MN.47: 4 residues within 4Å: Chain E: H.170 Chain X: H.73, E.77, H.145 5 PLIP interactions: 3 interactions with chain X, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: X:H.73, X:E.77, X:H.145, E:H.170, H2O.7 MN.48: 4 residues within 4Å: Chain K: H.74 Chain X: H.47, H.169, E.173 5 PLIP interactions: 4 interactions with chain X, 1 interactions with chain K Metal complexes: X:H.47, X:H.169, X:E.173, X:E.173, K:H.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Witek, W. et al., Cryo-EM and crystal structures of a herbicide development target, HISN5. To Be Published

Release Date

2021-06-02

Peptides

Imidazoleglycerol-phosphate dehydratase: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
V

V
W

W
X

X
Y

Imidazoleglycerol-phosphate dehydratase