SMTL ID : 3qo6.1

Crystal structure analysis of the plant protease Deg1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

12 x UNK- UNK- UNK- UNK- UNK- UNK- UNK: peptide(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 12 residues within 4Å: Chain A: H.71, N.176, P.177, G.178, S.180, T.196, A.197, I.198, Y.199, S.200, P.201 Chain B: F.138 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.199, A:P.201, B:F.138 Hydrogen bonds: A:G.178, A:T.196, A:I.198, A:I.198, A:S.200, A:S.200 UNK-UNK-UNK-UNK-UNK-UNK-UNK.2: 11 residues within 4Å: Chain B: H.71, S.157, N.176, P.177, G.178, N.179, S.180, T.196, A.197, I.198, Y.199 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.199 Hydrogen bonds: B:G.178, B:N.179, B:S.180, B:T.196, B:I.198, B:I.198 UNK-UNK-UNK-UNK-UNK-UNK-UNK.3: 10 residues within 4Å: Chain C: H.71, N.176, P.177, G.178, N.179, S.180, T.196, A.197, I.198, Y.199 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.199 Hydrogen bonds: C:G.178, C:N.179, C:S.180, C:T.196, C:I.198, C:I.198 UNK-UNK-UNK-UNK-UNK-UNK-UNK.4: 8 residues within 4Å: Chain A: R.163, I.234, L.235, G.236, I.237, K.238, F.239, Y.301 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.239, A:F.239, A:Y.301 Hydrogen bonds: A:L.235, A:G.236, A:I.237, A:I.237, A:I.237, A:F.239, A:Y.301 UNK-UNK-UNK-UNK-UNK-UNK-UNK.5: 10 residues within 4Å: Chain B: P.233, I.234, L.235, G.236, I.237, K.238, F.239, L.300, Y.301, L.304 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.239, B:F.239, B:L.300 Hydrogen bonds: B:L.235, B:G.236, B:I.237, B:I.237, B:I.237, B:F.239, B:F.239, B:Y.301 UNK-UNK-UNK-UNK-UNK-UNK-UNK.6: 7 residues within 4Å: Chain C: I.234, L.235, G.236, I.237, K.238, F.239, Y.301 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.237, C:F.239, C:F.239 Hydrogen bonds: C:L.235, C:G.236, C:I.237, C:I.237, C:I.237, C:F.239, C:F.239, C:Y.301 UNK-UNK-UNK-UNK-UNK-UNK-UNK.7: 12 residues within 4Å: Chain D: H.71, N.176, P.177, G.178, S.180, T.196, A.197, I.198, Y.199, S.200, P.201 Chain E: F.138 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.199, D:P.201, E:F.138 Hydrogen bonds: D:G.178, D:T.196, D:I.198, D:I.198, D:S.200, D:S.200 UNK-UNK-UNK-UNK-UNK-UNK-UNK.8: 11 residues within 4Å: Chain E: H.71, S.157, N.176, P.177, G.178, N.179, S.180, T.196, A.197, I.198, Y.199 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:Y.199 Hydrogen bonds: E:G.178, E:N.179, E:S.180, E:T.196, E:I.198, E:I.198 UNK-UNK-UNK-UNK-UNK-UNK-UNK.9: 10 residues within 4Å: Chain F: H.71, N.176, P.177, G.178, N.179, S.180, T.196, A.197, I.198, Y.199 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.199 Hydrogen bonds: F:G.178, F:N.179, F:S.180, F:T.196, F:I.198, F:I.198 UNK-UNK-UNK-UNK-UNK-UNK-UNK.10: 8 residues within 4Å: Chain D: R.163, I.234, L.235, G.236, I.237, K.238, F.239, Y.301 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.239, D:F.239, D:Y.301 Hydrogen bonds: D:L.235, D:G.236, D:I.237, D:I.237, D:F.239, D:F.239 UNK-UNK-UNK-UNK-UNK-UNK-UNK.11: 10 residues within 4Å: Chain E: P.233, I.234, L.235, G.236, I.237, K.238, F.239, L.300, Y.301, L.304 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.239, E:F.239, E:L.300 Hydrogen bonds: E:L.235, E:G.236, E:I.237, E:I.237, E:F.239, E:F.239, E:Y.301, E:Y.301 UNK-UNK-UNK-UNK-UNK-UNK-UNK.12: 7 residues within 4Å: Chain F: I.234, L.235, G.236, I.237, K.238, F.239, Y.301 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:I.237, F:F.239, F:F.239 Hydrogen bonds: F:L.235, F:G.236, F:I.237, F:I.237, F:F.239, F:F.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kley, J. et al., Structural adaptation of the plant protease Deg1 to repair photosystem II during light exposure. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-05-04

Peptides

Protease Do-like 1, chloroplastic: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Protease Do-like 1, chloroplastic