SMTL ID : 8pmm.1

Structure of Nal1 protein, allele SPIKE from japonica rice, construct 31-458

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: R.95, I.96, R.97, K.98, V.111, R.113, K.114, V.115, H.116, K.117, L.120, Q.124, C.125, L.126, V.140, D.141, V.142 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:I.96, A:K.98, A:V.115, A:K.117, A:Q.124, A:L.126, A:V.142 Water bridges: A:R.97, A:R.97, A:K.98, A:G.99, A:H.116, A:L.392 Salt bridges: A:R.95, A:R.95, A:R.97, A:K.98, A:K.98, A:K.114, A:K.114, A:K.114 ATP.4: 20 residues within 4Å: Chain B: F.86, R.95, I.96, R.97, K.98, V.111, R.113, K.114, V.115, H.116, K.117, L.120, Q.124, C.125, L.126, V.140, D.141, V.142 Chain C: P.231 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.98, B:V.115, B:K.117, B:Q.124, B:L.126, B:V.142 Water bridges: B:I.96, B:G.99 Salt bridges: B:R.95, B:R.95, B:R.97, B:K.114, B:K.114, B:K.114 ATP.6: 20 residues within 4Å: Chain A: P.231 Chain C: F.86, R.95, I.96, R.97, K.98, V.111, R.113, K.114, V.115, H.116, K.117, L.120, Q.124, C.125, L.126, V.140, D.141, V.142 Ligands: MG.7 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:F.86, C:K.98, C:V.115, C:K.117, C:L.126, C:V.142 Water bridges: C:R.97, C:R.97, C:R.97, C:R.97, C:G.99, C:K.114, C:K.114, C:L.392 Salt bridges: C:R.95, C:R.95, C:R.97, C:K.114, C:K.114, C:K.114 ATP.8: 18 residues within 4Å: Chain D: R.95, I.96, R.97, K.98, V.111, R.113, K.114, V.115, H.116, K.117, L.120, Q.124, C.125, L.126, V.140, D.141, V.142 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:I.96, D:K.98, D:V.115, D:K.117, D:Q.124, D:L.126, D:V.142 Water bridges: D:R.97, D:R.97, D:K.98, D:G.99, D:L.392 Salt bridges: D:R.95, D:R.95, D:R.97, D:K.98, D:K.98, D:K.114, D:K.114, D:K.114 ATP.11: 20 residues within 4Å: Chain E: F.86, R.95, I.96, R.97, K.98, V.111, R.113, K.114, V.115, H.116, K.117, L.120, Q.124, C.125, L.126, V.140, D.141, V.142 Chain F: P.231 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:K.98, E:V.115, E:K.117, E:Q.124, E:L.126, E:D.141, E:V.142 Water bridges: E:I.96, E:G.99 Salt bridges: E:R.95, E:R.95, E:R.97, E:K.114, E:K.114, E:K.114 ATP.13: 20 residues within 4Å: Chain D: P.231 Chain F: F.86, R.95, I.96, R.97, K.98, V.111, R.113, K.114, V.115, H.116, K.117, L.120, Q.124, C.125, L.126, V.140, D.141, V.142 Ligands: MG.14 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:F.86, F:K.98, F:V.115, F:K.117, F:L.126, F:V.142 Water bridges: F:R.97, F:R.97, F:R.97, F:R.97, F:G.99, F:K.114, F:K.114, F:L.392 Salt bridges: F:R.95, F:R.95, F:R.97, F:K.114, F:K.114, F:K.114

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: I.96, K.114, D.141 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.96, A:D.141, H2O.2 MG.5: 5 residues within 4Å: Chain B: I.96, K.114, D.141, V.142 Ligands: ATP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.96, B:D.141, H2O.11 MG.7: 4 residues within 4Å: Chain C: I.96, K.114, D.141 Ligands: ATP.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.96, C:D.141, H2O.18 MG.9: 4 residues within 4Å: Chain D: I.96, K.114, D.141 Ligands: ATP.8 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:I.96, D:D.141, H2O.25 MG.12: 5 residues within 4Å: Chain E: I.96, K.114, D.141, V.142 Ligands: ATP.11 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:I.96, E:D.141, H2O.35 MG.14: 4 residues within 4Å: Chain F: I.96, K.114, D.141 Ligands: ATP.13 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:I.96, F:D.141, H2O.42

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: Q.158, F.186, R.316 Chain C: R.113 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:R.316, C:R.113 PO4.10: 4 residues within 4Å: Chain D: Q.158, F.186, R.316 Chain F: R.113 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Salt bridges: D:R.316, F:R.113

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
A

E
B

F
C

Protein NARROW LEAF 1

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