SMTL ID : 7cjs.1 (1 other biounit)

structure of aquaporin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: T.144, A.146, V.147, G.148 Ligands: BOG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.146 Water bridges: A:G.148, A:G.148 NA.5: 4 residues within 4Å: Chain B: T.144, A.146, V.147, G.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.146 Water bridges: B:G.148 NA.9: 4 residues within 4Å: Chain C: T.144, A.146, V.147, G.148 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.146 Water bridges: C:G.148 NA.11: 4 residues within 4Å: Chain D: T.144, A.146, V.147, G.148 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.146, D:G.148

3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.2: 8 residues within 4Å: Chain A: T.144, R.145, A.146, V.147 Chain B: H.57, G.148, E.149 Ligands: NA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.145 Water bridges: A:R.145 BOG.6: 8 residues within 4Å: Chain A: P.118, W.120, H.121 Chain B: F.98, K.101, A.102, V.103, H.105 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.101, B:A.102 Salt bridges: B:H.105 Hydrogen bonds: A:H.121, A:H.121 Water bridges: A:W.120 BOG.12: 8 residues within 4Å: Chain D: H.119, W.120, L.123, V.124, G.191, W.193, I.194 Ligands: PG4.13 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.120, D:L.123, D:W.193 Hydrogen bonds: D:W.193 Water bridges: D:W.120

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 18 residues within 4Å: Chain A: I.42, G.45, L.46, V.49, L.153, S.157, C.160 Chain B: I.42, L.46, L.153 Chain D: I.42, G.45, L.46, V.49, G.156, S.157, C.160 Ligands: PG4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.157, A:S.157 PG4.4: 5 residues within 4Å: Chain A: S.30, P.106, V.107, D.108, V.109 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.31, A:D.108, A:D.108 PG4.7: 6 residues within 4Å: Chain B: W.208, V.209, F.212 Chain C: V.8, V.12 Ligands: PG4.8 No protein-ligand interaction detected (PLIP) PG4.8: 12 residues within 4Å: Chain B: V.127, I.128, F.131, S.205 Chain C: V.11, V.12, F.15, L.16, T.91, G.92, A.95 Ligands: PG4.7 No protein-ligand interaction detected (PLIP) PG4.10: 19 residues within 4Å: Chain B: I.42, G.45, L.46, V.49, G.156, S.157, C.160 Chain C: I.42, G.45, L.46, V.49, L.153, G.156, S.157, C.160 Chain D: I.42, L.46, L.153 Ligands: PG4.3 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.157, C:S.157 PG4.13: 7 residues within 4Å: Chain D: F.189, D.190, G.191, L.192, W.193, F.196 Ligands: BOG.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.191, D:L.192, D:W.193

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.14: 4 residues within 4Å: Chain D: R.75, W.79, P.83, W.86 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.79, D:W.79, D:W.79, D:P.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saitoh, Y. et al., Structural basis for high selectivity of a rice silicon channel Lsi1. Nat Commun (2021)

Release Date

2021-11-03

Peptides

Aquaporin NIP2-1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Aquaporin NIP2-1

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