SMTL ID : 8pn2.1

CryoEM structure of Nal1 protein, allele IR64, from Oryza sativa indica cultivar

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: F.113, R.122, I.123, R.124, K.125, V.138, R.140, K.141, V.142, H.143, K.144, L.147, Q.151, C.152, L.153, V.167, D.168, V.169 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.124, A:K.125, A:V.142, A:Q.151, A:L.153, A:V.169 Salt bridges: A:R.122, A:R.122, A:R.124, A:K.141, A:K.141, A:K.141 ATP.3: 18 residues within 4Å: Chain B: F.113, R.122, I.123, R.124, K.125, V.138, R.140, K.141, V.142, H.143, K.144, L.147, Q.151, L.153, V.167, D.168, V.169 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.124, B:K.125, B:V.142, B:Q.151, B:L.153, B:V.169 Salt bridges: B:R.122, B:R.122, B:R.124, B:K.141, B:K.141, B:K.141 ATP.5: 19 residues within 4Å: Chain C: F.113, R.122, I.123, R.124, K.125, V.138, R.140, K.141, V.142, H.143, K.144, L.147, Q.151, C.152, L.153, V.167, D.168, V.169 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:F.113, C:R.124, C:K.125, C:V.142, C:L.153, C:V.169 Salt bridges: C:R.122, C:R.122, C:R.124, C:K.141, C:K.141, C:K.141 ATP.7: 19 residues within 4Å: Chain D: F.113, R.122, I.123, R.124, K.125, V.138, R.140, K.141, V.142, H.143, K.144, L.147, Q.151, C.152, L.153, V.167, D.168, V.169 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:F.113, D:R.124, D:K.125, D:V.142, D:L.153, D:V.169 Salt bridges: D:R.122, D:R.122, D:R.124, D:K.141, D:K.141, D:K.141 ATP.9: 18 residues within 4Å: Chain E: F.113, R.122, I.123, R.124, K.125, V.138, R.140, K.141, V.142, H.143, K.144, L.147, Q.151, L.153, V.167, D.168, V.169 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:R.124, E:K.125, E:V.142, E:Q.151, E:L.153, E:V.169 Salt bridges: E:R.122, E:R.122, E:R.124, E:K.141, E:K.141, E:K.141 ATP.11: 19 residues within 4Å: Chain F: F.113, R.122, I.123, R.124, K.125, V.138, R.140, K.141, V.142, H.143, K.144, L.147, Q.151, C.152, L.153, V.167, D.168, V.169 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:R.124, F:K.125, F:V.142, F:Q.151, F:L.153, F:V.169 Salt bridges: F:R.122, F:R.122, F:R.124, F:K.141, F:K.141, F:K.141

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: I.123, K.141, D.168, V.169 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.123, A:D.168 MG.4: 5 residues within 4Å: Chain B: I.123, K.141, D.168, V.169 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:I.123, B:D.168 MG.6: 5 residues within 4Å: Chain C: I.123, K.141, D.168, V.169 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:I.123, C:D.168 MG.8: 5 residues within 4Å: Chain D: I.123, K.141, D.168, V.169 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:I.123, D:D.168 MG.10: 5 residues within 4Å: Chain E: I.123, K.141, D.168, V.169 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:I.123, E:D.168 MG.12: 5 residues within 4Å: Chain F: I.123, K.141, D.168, V.169 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:I.123, F:D.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, L.Y. et al., The catalytic triad of rice NARROW LEAF1 involves H234. Nat.Plants (2024)

Release Date

2024-04-17

Peptides

Protein NARROW LEAF 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Protein NARROW LEAF 1