SMTL ID : 7uqw.1

PCC6803 Cyanophycinase S132DAP covalently bound to cyanophycin dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

12 x 7ID: (2~{S})-4-[[(2~{S})-5-[[azanyl($l^{4}-azanylidene)methyl]amino]-1-$l^{1}-oxidanyl-1-oxidanylidene-pentan-2-yl]amino]-2-$l^{2}-azanyl-4-oxidanylidene-butanoic acid(Non-covalent)(Covalent)

7ID.1: 3 residues within 4Å: Chain A: G.99, R.178 Ligands: 7ID.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.178, A:R.178 7ID.2: 14 residues within 4Å: Chain A: G.98, G.99, D.100, Q.101, A.132, A.133, A.144, G.145, Q.173, H.174, R.178, R.180, R.183 Ligands: 7ID.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.99, A:G.99, A:Q.101, A:Q.101, A:A.133, A:Q.173, A:R.178, A:R.180, A:R.180 Water bridges: A:G.146, A:G.146, A:G.146, A:G.146 Salt bridges: A:D.100, A:R.180, A:R.183 7ID.4: 3 residues within 4Å: Chain B: G.99, R.178 Ligands: 7ID.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.178, B:R.178 7ID.5: 14 residues within 4Å: Chain B: G.98, G.99, D.100, Q.101, A.132, A.133, A.144, G.145, Q.173, H.174, R.178, R.180, R.183 Ligands: 7ID.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.99, B:G.99, B:Q.101, B:Q.101, B:Q.101, B:A.133, B:Q.173, B:R.178, B:R.180, B:R.180 Water bridges: B:G.99, B:G.146 Salt bridges: B:D.100, B:R.180, B:R.183 7ID.11: 3 residues within 4Å: Chain C: G.99, R.178 Ligands: 7ID.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.178, C:R.178 7ID.12: 14 residues within 4Å: Chain C: G.98, G.99, D.100, Q.101, A.132, A.133, A.144, G.145, Q.173, H.174, R.178, R.180, R.183 Ligands: 7ID.11 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.99, C:G.99, C:Q.101, C:Q.101, C:A.133, C:Q.173, C:R.178, C:R.180, C:R.180 Water bridges: C:G.146, C:G.146, C:G.146, C:G.146 Salt bridges: C:D.100, C:R.180, C:R.183 7ID.14: 3 residues within 4Å: Chain D: G.99, R.178 Ligands: 7ID.15 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.178, D:R.178 7ID.15: 14 residues within 4Å: Chain D: G.98, G.99, D.100, Q.101, A.132, A.133, A.144, G.145, Q.173, H.174, R.178, R.180, R.183 Ligands: 7ID.14 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.99, D:G.99, D:Q.101, D:Q.101, D:Q.101, D:A.133, D:Q.173, D:R.178, D:R.180, D:R.180 Water bridges: D:G.99, D:G.146 Salt bridges: D:D.100, D:R.180, D:R.183 7ID.21: 3 residues within 4Å: Chain E: G.99, R.178 Ligands: 7ID.22 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.178, E:R.178 7ID.22: 14 residues within 4Å: Chain E: G.98, G.99, D.100, Q.101, A.132, A.133, A.144, G.145, Q.173, H.174, R.178, R.180, R.183 Ligands: 7ID.21 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.99, E:G.99, E:Q.101, E:Q.101, E:Q.101, E:A.133, E:Q.173, E:R.178, E:R.180, E:R.180 Water bridges: E:G.146 Salt bridges: E:D.100, E:R.180, E:R.183 7ID.25: 3 residues within 4Å: Chain F: G.99, R.178 Ligands: 7ID.26 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.178, F:R.178 7ID.26: 14 residues within 4Å: Chain F: G.98, G.99, D.100, Q.101, A.132, A.133, A.144, G.145, Q.173, H.174, R.178, R.180, R.183 Ligands: 7ID.25 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.99, F:G.99, F:Q.101, F:Q.101, F:Q.101, F:A.133, F:Q.173, F:R.178, F:R.180, F:R.180 Water bridges: F:G.146 Salt bridges: F:D.100, F:R.180, F:R.183

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

SO4.3: 1 residues within 4Å: Chain A: R.209 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.209 SO4.13: 1 residues within 4Å: Chain C: R.209 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.209

14 x ARF: FORMAMIDE(Non-covalent)

ARF.6: 6 residues within 4Å: Chain B: S.61, G.64, V.65, K.66 Chain F: R.85, E.89 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:E.89, F:E.89, B:V.65 ARF.7: 4 residues within 4Å: Chain B: L.102, C.105, A.160, V.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.161, B:V.161 ARF.8: 7 residues within 4Å: Chain B: P.7, A.8, I.9, V.121, G.124, I.126, R.209 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.121, B:R.209 ARF.9: 2 residues within 4Å: Chain B: Y.231, T.232 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.232 ARF.10: 4 residues within 4Å: Chain B: R.154, A.234, A.235, V.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.234 ARF.16: 6 residues within 4Å: Chain D: S.61, G.64, V.65, K.66 Chain E: R.85, E.89 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:E.89, D:V.65 ARF.17: 4 residues within 4Å: Chain D: L.102, C.105, A.160, V.161 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.161, D:V.161 ARF.18: 7 residues within 4Å: Chain D: P.7, A.8, I.9, V.121, G.124, I.126, R.209 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.121, D:R.209 ARF.19: 2 residues within 4Å: Chain D: Y.231, T.232 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.232 ARF.20: 4 residues within 4Å: Chain D: R.154, A.234, A.235, V.237 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.234 ARF.23: 6 residues within 4Å: Chain E: P.7, A.8, V.121, G.124, I.126, R.209 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:V.121, E:R.209 ARF.24: 6 residues within 4Å: Chain E: G.14, A.15, E.16, K.18, Y.56, A.132 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:A.15, E:E.16, E:K.18, E:Y.56, E:Y.56 ARF.27: 6 residues within 4Å: Chain F: P.7, A.8, V.121, G.124, I.126, R.209 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.121, F:R.209 ARF.28: 6 residues within 4Å: Chain F: G.14, A.15, E.16, K.18, Y.56, A.132 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:A.15, F:E.16, F:K.18, F:Y.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharon, I. et al., The structure of cyanophycinase in complex with a cyanophycin degradation intermediate. Biochim Biophys Acta Gen Subj (2022)

Release Date

2022-08-10

Peptides

Cyanophycinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
C

F
C

Cyanophycinase