SMTL ID : 8egl.2 (1 other biounit)

Crystal Structure of Guanylate kinase from Pseudomonas aeruginosa PAO1 in complex with GMP and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 13 residues within 4Å: Chain A: S.12, G.13, A.14, G.15, K.16, T.17, S.18, R.131, R.135, N.166, D.167, F.169 Chain D: P.28 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.13, A:A.14, A:G.15, A:K.16, A:T.17, A:T.17, A:S.18, A:S.18, A:R.131, A:N.166, A:D.167 Water bridges: A:P.11, A:K.16, A:K.16, A:T.17, A:T.17, A:R.135, A:F.169, A:F.169, D:R.31 Salt bridges: A:K.16, A:R.135, A:R.135 pi-Cation interactions: A:R.131 ADP.3: 14 residues within 4Å: Chain A: P.28 Chain B: P.11, S.12, G.13, A.14, G.15, K.16, T.17, S.18, R.131, R.135, N.166, D.167, F.169 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.13, B:A.14, B:G.15, B:K.16, B:T.17, B:T.17, B:S.18, B:S.18, B:N.166, B:D.167 Water bridges: B:S.12, B:T.17, A:R.31, A:R.31 Salt bridges: B:R.135, B:R.135 pi-Cation interactions: B:R.131 ADP.5: 16 residues within 4Å: Chain C: P.11, S.12, G.13, A.14, G.15, K.16, T.17, S.18, R.131, R.135, N.166, D.167, F.169 Chain F: P.28, E.29, R.31 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:P.11, C:G.13, C:A.14, C:G.15, C:K.16, C:T.17, C:T.17, C:S.18, C:S.18, C:N.166, C:D.167, F:R.31 Water bridges: C:K.16, C:R.131, C:R.131, C:R.131, C:F.169, C:F.169 Salt bridges: C:K.16 pi-Cation interactions: C:R.131 ADP.7: 14 residues within 4Å: Chain B: P.28, E.29 Chain D: S.12, G.13, A.14, G.15, K.16, T.17, S.18, R.131, R.135, N.166, D.167, F.169 24 PLIP interactions: 23 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.13, D:A.14, D:G.15, D:K.16, D:T.17, D:T.17, D:S.18, D:S.18, D:N.166, D:D.167 Water bridges: D:P.11, D:K.16, D:T.17, D:R.131, D:R.131, D:R.131, D:R.135, D:F.169, D:F.169, B:R.31 Salt bridges: D:K.16, D:R.135, D:R.135 pi-Cation interactions: D:R.131 ADP.9: 15 residues within 4Å: Chain C: P.28, E.29 Chain E: P.11, S.12, G.13, A.14, G.15, K.16, T.17, S.18, R.131, R.135, N.166, D.167, F.169 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:P.11, E:G.13, E:A.14, E:G.15, E:K.16, E:T.17, E:T.17, E:S.18, E:S.18, E:S.18, E:N.166, E:D.167 Water bridges: E:K.16 Salt bridges: E:K.16, E:R.135, E:R.135 pi-Cation interactions: E:R.131 ADP.11: 14 residues within 4Å: Chain E: P.28, E.29 Chain F: S.12, G.13, A.14, G.15, K.16, T.17, S.18, R.131, R.135, N.166, D.167, F.169 22 PLIP interactions: 22 interactions with chain F Hydrogen bonds: F:P.11, F:G.13, F:A.14, F:G.15, F:K.16, F:T.17, F:T.17, F:S.18, F:S.18, F:N.166, F:D.167 Water bridges: F:K.16, F:K.16, F:K.16, F:T.17, F:R.131, F:F.169, F:F.169 Salt bridges: F:K.16, F:R.135, F:R.135 pi-Cation interactions: F:R.131

6 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.2: 16 residues within 4Å: Chain A: K.16, S.35, R.39, R.42, Y.51, E.70, A.72, V.74, Y.79, G.80, T.81, E.99, I.100, D.101, G.104, R.146 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.10, A:K.16, A:K.16, A:S.35, A:Y.51, A:Y.79, A:D.101, A:G.104 Water bridges: A:R.42, A:R.42, A:R.135 Salt bridges: A:R.39, A:R.42, A:E.70, A:D.101, A:R.146 5GP.4: 15 residues within 4Å: Chain B: K.16, S.35, R.39, Y.51, E.70, A.72, V.74, Y.79, G.80, T.81, E.99, I.100, D.101, G.104, R.146 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.16, B:K.16, B:S.35, B:Y.51, B:Y.79, B:Y.79, B:D.101, B:G.104 Water bridges: B:R.146, B:R.146 Salt bridges: B:R.39, B:E.70, B:D.101, B:R.146 5GP.6: 17 residues within 4Å: Chain C: A.10, K.16, S.35, R.39, R.42, Y.51, E.70, A.72, V.74, Y.79, G.80, T.81, E.99, I.100, D.101, G.104, R.146 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:K.16, C:K.16, C:S.35, C:Y.51, C:Y.79, C:T.81, C:D.101, C:G.104 Salt bridges: C:R.39, C:R.42, C:E.70, C:D.101, C:R.146 5GP.8: 17 residues within 4Å: Chain D: K.16, S.35, R.39, R.42, Y.51, E.70, A.72, V.74, F.75, Y.79, G.80, T.81, E.99, I.100, D.101, G.104, R.146 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:K.16, D:K.16, D:S.35, D:Y.51, D:Y.79, D:D.101, D:G.104 Water bridges: D:R.42, D:R.42 Salt bridges: D:R.39, D:R.42, D:E.70, D:D.101, D:R.146 5GP.10: 16 residues within 4Å: Chain E: A.10, K.16, S.35, Y.51, E.70, A.72, V.74, F.75, Y.79, G.80, T.81, E.99, I.100, D.101, G.104, E.153 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:K.16, E:K.16, E:S.35, E:Y.51, E:T.81, E:D.101, E:G.104, E:E.153 Water bridges: E:E.45 Salt bridges: E:E.70, E:D.101 5GP.12: 17 residues within 4Å: Chain F: A.10, K.16, S.35, R.39, R.42, Y.51, E.70, A.72, V.74, Y.79, G.80, T.81, E.99, I.100, D.101, G.104, R.146 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:A.10, F:K.16, F:K.16, F:S.35, F:Y.51, F:T.81, F:D.101, F:G.104 Water bridges: F:R.135 Salt bridges: F:R.39, F:R.42, F:E.70, F:D.101, F:R.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of Guanylate kinase from Pseudomonas aeruginosa PAO1 in complex with GMP and ADP. to be published

Release Date

2022-09-28

Peptides

Guanylate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

D
G

E
H

F
I

Guanylate kinase

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