SMTL ID : 8pmi.1

Structure of Nal1 indica cultivar IR64, construct 36-458 in presence of peptide from FZP protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: R.85, I.86, R.87, K.88, V.101, R.103, K.104, V.105, H.106, K.107, L.110, Q.114, L.116, V.130, D.131, V.132 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.88, A:V.105, A:Q.114, A:L.116, A:D.131, A:V.132 Salt bridges: A:R.85, A:R.85, A:R.87, A:K.88, A:K.104, A:K.104, A:K.104 ATP.5: 19 residues within 4Å: Chain B: R.85, I.86, R.87, K.88, V.101, R.103, K.104, V.105, H.106, K.107, L.110, Q.114, C.115, L.116, V.130, D.131, V.132 Ligands: MG.6, MG.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.88, B:V.105, B:Q.114, B:L.116, B:V.132 Salt bridges: B:R.85, B:R.85, B:R.87, B:K.104, B:K.104, B:K.104 ATP.12: 18 residues within 4Å: Chain C: R.85, I.86, R.87, K.88, V.101, R.103, K.104, V.105, H.106, K.107, L.110, Q.114, C.115, L.116, V.130, D.131, V.132 Ligands: MG.13 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:I.86, C:K.88, C:G.89, C:V.105, C:Q.114, C:L.116, C:V.132 Salt bridges: C:R.85, C:R.85, C:R.87, C:K.104, C:K.104 ATP.16: 17 residues within 4Å: Chain D: R.85, I.86, R.87, K.88, V.101, R.103, K.104, V.105, H.106, K.107, L.110, Q.114, L.116, V.130, D.131, V.132 Ligands: MG.17 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.87, D:K.88, D:V.105, D:K.107, D:L.116, D:D.131, D:D.131, D:V.132 Salt bridges: D:R.85, D:R.85, D:R.87, D:K.104, D:K.104 ATP.20: 18 residues within 4Å: Chain E: R.85, I.86, R.87, K.88, V.101, R.103, K.104, V.105, H.106, K.107, L.110, Q.114, C.115, L.116, V.130, D.131, V.132 Ligands: MG.21 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:K.88, E:V.105, E:Q.114, E:L.116, E:V.132, E:V.132 Salt bridges: E:R.85, E:R.85, E:K.104, E:K.104 ATP.23: 18 residues within 4Å: Chain F: R.85, I.86, R.87, K.88, V.101, R.103, K.104, V.105, H.106, K.107, L.110, Q.114, C.115, L.116, V.130, D.131, V.132 Ligands: MG.24 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:F.76, F:K.88, F:V.105, F:L.116, F:D.131, F:V.132 Salt bridges: F:R.85, F:R.85, F:R.87, F:K.104, F:K.104, F:K.104

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: I.86, R.87, D.131, V.132 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.86, A:D.131 MG.6: 5 residues within 4Å: Chain B: I.86, K.104, D.131, V.132 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:I.86, B:D.131 MG.7: 4 residues within 4Å: Chain B: K.104, K.381, L.382 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain C: I.86, R.87, D.131, V.132 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:I.86, C:D.131 MG.17: 5 residues within 4Å: Chain D: I.86, K.104, D.131, V.132 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:I.86, D:D.131 MG.21: 5 residues within 4Å: Chain E: I.86, K.104, D.131, V.132 Ligands: ATP.20 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:I.86, E:D.131, E:D.131 MG.24: 6 residues within 4Å: Chain F: I.86, R.87, K.104, D.131, V.132 Ligands: ATP.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:I.86, F:D.131

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: M.149, S.151, L.153, V.154, S.308, G.309, H.310 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.151, A:H.310 SO4.4: 8 residues within 4Å: Chain A: P.141, Q.143, T.175, F.176, H.199, V.200, S.350, G.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.143, A:H.199, A:S.350 SO4.8: 5 residues within 4Å: Chain B: S.151, V.154, S.308, G.309, H.310 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.151, B:S.151, B:H.310, B:H.310 SO4.9: 4 residues within 4Å: Chain B: G.53, Q.55, N.57, D.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.53 SO4.10: 3 residues within 4Å: Chain B: K.52, Q.55, D.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.55, B:D.93 Salt bridges: B:K.52 SO4.11: 4 residues within 4Å: Chain B: G.89, M.316, G.338, L.382 No protein-ligand interaction detected (PLIP) SO4.14: 6 residues within 4Å: Chain C: P.141, Q.143, F.176, V.200, G.348, S.350 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.143, C:G.348, C:S.350, C:S.350 SO4.15: 6 residues within 4Å: Chain C: S.151, L.153, V.154, S.308, G.309, H.310 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.151, C:S.151, C:H.310, C:H.310 SO4.18: 6 residues within 4Å: Chain D: S.151, L.153, V.154, S.308, G.309, H.310 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.151, D:H.310 SO4.19: 6 residues within 4Å: Chain D: Q.143, F.176, V.200, G.348, S.350, G.372 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.143, D:G.348, D:S.350 SO4.25: 5 residues within 4Å: Chain F: S.151, L.153, S.308, G.309, H.310 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.151, F:H.310 SO4.26: 9 residues within 4Å: Chain F: P.141, Q.143, P.145, T.175, F.176, V.200, G.348, S.350, G.372 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.175, F:G.348, F:S.350

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.22: 5 residues within 4Å: Chain E: G.30, R.31, N.33, Y.34, Y.244 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.30

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

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