SMTL ID : 9jaf.1

GMPK in complex with GMP and sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.58, R.59 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.59 Water bridges: A:E.60 SO4.2: 8 residues within 4Å: Chain A: S.14, G.15, A.16, G.17, K.18, S.19, T.20, R.138 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.15, A:G.17, A:K.18, A:S.19, A:S.19, A:T.20, A:R.138 SO4.3: 4 residues within 4Å: Chain A: R.42, N.43, R.45, N.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.43, A:R.45, A:N.80 Water bridges: A:E.141 SO4.4: 4 residues within 4Å: Chain A: E.28, H.29, Y.179, K.183 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.28, A:E.28, A:Y.179, A:Y.179 Salt bridges: A:H.29, A:K.183 SO4.5: 2 residues within 4Å: Chain A: E.60 Ligands: SO4.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.60 SO4.6: 1 residues within 4Å: Chain A: H.74 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.74 SO4.7: 4 residues within 4Å: Chain A: N.96, R.97 Chain B: T.58, V.61 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.58, A:N.96 Water bridges: B:T.58, A:M.95, A:R.97 Salt bridges: A:R.97 SO4.10: 2 residues within 4Å: Chain B: S.174, L.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.175 Water bridges: B:D.176 SO4.11: 4 residues within 4Å: Chain A: N.50 Chain B: S.30, G.31, R.97 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.31, A:N.50 Salt bridges: B:R.97 SO4.12: 6 residues within 4Å: Chain B: G.15, A.16, G.17, K.18, S.19, T.20 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.15, B:G.17, B:K.18, B:S.19, B:T.20, B:T.20

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

5GP.8: 18 residues within 4Å: Chain A: G.12, S.14, K.18, S.38, R.42, Y.54, E.73, A.75, F.77, Y.82, G.83, T.84, D.102, V.103, D.104, G.107, R.138, R.149 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.14, A:K.18, A:S.38, A:Y.54, A:D.102, A:D.104, A:R.138 Water bridges: A:G.12 Salt bridges: A:R.42, A:E.73, A:D.104, A:R.149 5GP.13: 16 residues within 4Å: Chain B: S.14, K.18, S.38, R.42, R.45, Y.54, E.73, A.75, F.77, Y.82, G.83, T.84, D.102, V.103, D.104, G.107 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.14, B:K.18, B:S.38, B:Y.54, B:Y.82, B:D.102, B:D.104, B:G.107 Water bridges: B:R.45, B:D.156 Salt bridges: B:R.42, B:R.45, B:E.73, B:D.104

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: S.3, G.4, R.6, R.117 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.4, A:R.6, A:R.117, A:R.117 Water bridges: A:R.117 GOL.14: 4 residues within 4Å: Chain B: L.22, F.35, K.52, D.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.53 GOL.15: 3 residues within 4Å: Chain B: T.58, R.59, E.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.59, B:E.60 Water bridges: B:T.41 GOL.16: 3 residues within 4Å: Chain B: R.42, N.43, N.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.43, B:N.80 Water bridges: B:T.41, B:N.43, B:N.80 GOL.17: 3 residues within 4Å: Chain B: E.48, E.49, N.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.48, B:N.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Comprehensive profiling of the catalytic conformations of human Guanylate kinase. To Be Published

Release Date

2025-09-03

Peptides

Guanylate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Guanylate kinase

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