SMTL ID : 5gnd.1

Structure of Deg protease HhoA from Synechocystis sp. PCC 6803

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x UNK- UNK- UNK- UNK- TRP: UNK-UNK-UNK-UNK-TRP(Non-covalent)

UNK-UNK-UNK-UNK-TRP.1: 11 residues within 4Å: Chain A: Y.234, I.235, G.236, V.237, Q.238, M.239, M.240, N.241, L.272, Q.303, V.306 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.234, A:Y.234, A:I.235, A:Q.303, A:V.306, A:V.306 Hydrogen bonds: A:M.239, A:N.241, A:N.241, A:Q.303 UNK-UNK-UNK-UNK-TRP.4: 11 residues within 4Å: Chain B: Y.234, I.235, G.236, V.237, Q.238, M.239, M.240, N.241, L.272, Q.303, V.306 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.234, B:Y.234, B:I.235, B:Q.303, B:V.306, B:V.306 Hydrogen bonds: B:M.239, B:N.241, B:N.241, B:Q.303 UNK-UNK-UNK-UNK-TRP.7: 11 residues within 4Å: Chain C: Y.234, I.235, G.236, V.237, Q.238, M.239, M.240, N.241, L.272, Q.303, V.306 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.234, C:Y.234, C:I.235, C:Q.303, C:V.306, C:V.306 Hydrogen bonds: C:M.239, C:N.241, C:N.241, C:Q.303 UNK-UNK-UNK-UNK-TRP.10: 11 residues within 4Å: Chain D: Y.234, I.235, G.236, V.237, Q.238, M.239, M.240, N.241, L.272, Q.303, V.306 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:Y.234, D:Y.234, D:I.235, D:Q.303, D:V.306, D:V.306 Hydrogen bonds: D:M.239, D:N.241, D:N.241, D:Q.303 UNK-UNK-UNK-UNK-TRP.13: 11 residues within 4Å: Chain E: Y.234, I.235, G.236, V.237, Q.238, M.239, M.240, N.241, L.272, Q.303, V.306 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Y.234, E:Y.234, E:I.235, E:Q.303, E:V.306, E:V.306 Hydrogen bonds: E:M.239, E:N.241, E:N.241, E:Q.303 UNK-UNK-UNK-UNK-TRP.16: 11 residues within 4Å: Chain F: Y.234, I.235, G.236, V.237, Q.238, M.239, M.240, N.241, L.272, Q.303, V.306 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:Y.234, F:Y.234, F:I.235, F:Q.303, F:V.306, F:V.306 Hydrogen bonds: F:M.239, F:N.241, F:N.241, F:Q.303

6 x ZN: ZINC ION(Non-functional Binders)

ZN.2: 2 residues within 4Å: Ligands: ZN.5, ZN.8 No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Ligands: ZN.2, ZN.8 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Ligands: ZN.2, ZN.5 No protein-ligand interaction detected (PLIP) ZN.11: 2 residues within 4Å: Ligands: ZN.14, ZN.17 No protein-ligand interaction detected (PLIP) ZN.14: 2 residues within 4Å: Ligands: ZN.11, ZN.17 No protein-ligand interaction detected (PLIP) ZN.17: 2 residues within 4Å: Ligands: ZN.11, ZN.14 No protein-ligand interaction detected (PLIP)

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

NA.3: 2 residues within 4Å: Ligands: NA.6, NA.9 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Water bridges: B:L.149, B:L.149, A:L.149, A:L.149, C:L.149, C:L.149 NA.6: 2 residues within 4Å: Ligands: NA.3, NA.9 No protein-ligand interaction detected (PLIP) NA.9: 2 residues within 4Å: Ligands: NA.3, NA.6 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Water bridges: B:L.149, B:L.149, A:L.149, C:L.149 NA.12: 2 residues within 4Å: Ligands: NA.15, NA.18 No protein-ligand interaction detected (PLIP) NA.15: 2 residues within 4Å: Ligands: NA.12, NA.18 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Water bridges: D:L.149, F:L.149 NA.18: 2 residues within 4Å: Ligands: NA.12, NA.15 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, 2 interactions with chain F Water bridges: D:L.149, D:L.149, E:L.149, E:L.149, F:L.149, F:L.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, W. et al., Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803. Febs Lett. (2016)

Release Date

2016-09-21

Peptides

Putative serine protease HhoA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Putative serine protease HhoA

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