SMTL ID : 8pmg.1

Structure of Nal1 indica cultivar IR64, construct 36-458

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.87, A:K.88, A:V.105, A:K.107, A:Q.114, A:L.116, A:V.132 Salt bridges: A:R.85, A:R.85, A:R.87, A:K.104, A:K.104 ATP.5: 17 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, L.116, V.130, D.131, V.132 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.88, B:G.89, 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 ATP.8: 19 residues within 4Å: Chain C: F.76, 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.9 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:F.76, C:K.88, C:V.105, C:L.116, C:V.132 Salt bridges: C:R.85, C:R.85, C:R.87, C:K.88, C:K.104, C:K.104, C:K.104 ATP.10: 18 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, C.115, L.116, V.130, D.131, V.132 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.88, D:V.105, D:Q.114, D:L.116, D:V.132 Salt bridges: D:R.85, D:R.85, D:R.87, D:K.104, D:K.104, D:K.104 ATP.14: 17 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, L.116, V.130, D.131, V.132 Ligands: MG.15 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 Salt bridges: E:R.85, E:R.85, E:R.87, E:K.104, E:K.104 ATP.17: 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.18 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:K.88, F:V.105, F:Q.114, F:L.116, F:V.132 Salt bridges: F:R.85, F:R.85, F:R.87, F:K.104, F:K.104, F:K.104

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: I.86, D.131, V.132 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.86 MG.6: 4 residues within 4Å: Chain B: I.86, D.131, V.132 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:I.86 MG.9: 6 residues within 4Å: Chain C: I.86, R.87, K.104, D.131, V.132 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:I.86, C:D.131 MG.11: 5 residues within 4Å: Chain D: I.86, R.87, D.131, V.132 Ligands: ATP.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:I.86, D:D.131, D:D.131 MG.15: 4 residues within 4Å: Chain E: I.86, D.131, V.132 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:I.86, E:D.131 MG.18: 4 residues within 4Å: Chain F: I.86, D.131, V.132 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:I.86

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

PO4.3: 9 residues within 4Å: Chain A: S.166, G.180, A.181, I.182, T.273, I.281, L.353, I.408, I.409 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.182 PO4.7: 6 residues within 4Å: Chain B: S.151, L.153, 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:S.308, B:H.310 PO4.12: 5 residues within 4Å: Chain D: M.149, S.151, V.154, G.309, H.310 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.151, D:S.151, D:H.310 PO4.13: 9 residues within 4Å: Chain D: S.166, G.180, A.181, I.182, T.273, V.275, I.281, I.408, I.409 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:I.182, D:T.273 PO4.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.19: 5 residues within 4Å: Chain F: S.151, L.153, S.308, G.309, H.310 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.151, F:H.310, F:H.310

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: G.30, N.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.30, A:N.33

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

Related Entries With Identical Sequence