SMTL ID : 9jag.1

GMPK in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: S.30, G.31, R.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.31 Water bridges: A:I.32 Salt bridges: A:R.97 SO4.2: 3 residues within 4Å: Chain A: R.42, N.43, N.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.43, A:N.43, A:N.80, A:N.80 SO4.3: 4 residues within 4Å: Chain A: S.127, L.128, H.129 Chain B: S.78 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.128, A:H.129, B:S.78, B:S.78 SO4.9: 3 residues within 4Å: Chain B: S.30, G.31, R.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.31 Water bridges: B:I.32 Salt bridges: B:R.97 SO4.10: 3 residues within 4Å: Chain B: R.42, N.43, N.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.43, B:N.43, B:N.80, B:N.80 SO4.11: 4 residues within 4Å: Chain A: S.78 Chain B: S.127, L.128, H.129 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.78, A:S.78, B:L.128, B:H.129

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: E.28, H.29, Q.194 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.28, A:Q.194 GOL.5: 4 residues within 4Å: Chain A: H.39, N.50, Y.55, F.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.39, A:N.50, A:N.50, A:F.56 GOL.6: 6 residues within 4Å: Chain A: S.36, E.73, T.84, L.101, D.102, V.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.36, A:E.73, A:T.84, A:D.102 GOL.7: 4 residues within 4Å: Chain A: H.29, K.183, Q.194 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.29, A:Q.194 Water bridges: A:K.183, A:Q.194 GOL.12: 4 residues within 4Å: Chain B: E.28, H.29, Q.194 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.28, B:Q.194 GOL.13: 4 residues within 4Å: Chain B: H.39, N.50, Y.55, F.56 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.39, B:N.50, B:N.50, B:F.56 GOL.14: 6 residues within 4Å: Chain B: S.36, E.73, T.84, L.101, D.102, V.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.36, B:E.73, B:D.102 GOL.15: 4 residues within 4Å: Chain B: H.29, K.183, Q.194 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.29, B:Q.194 Water bridges: B:K.183, B:Q.194

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

ADP.8: 13 residues within 4Å: Chain A: P.13, S.14, G.15, A.16, G.17, K.18, S.19, T.20, R.134, Q.137, R.138, N.172, L.175 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.15, A:A.16, A:G.17, A:K.18, A:S.19, A:T.20, A:T.20, A:R.134, A:Q.137, A:N.172 Salt bridges: A:K.18 pi-Cation interactions: A:R.134 ADP.16: 13 residues within 4Å: Chain B: P.13, S.14, G.15, A.16, G.17, K.18, S.19, T.20, R.134, Q.137, R.138, N.172, L.175 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.15, B:A.16, B:G.17, B:K.18, B:S.19, B:T.20, B:T.20, B:R.134, B:Q.137, B:N.172 Salt bridges: B:K.18 pi-Cation interactions: B:R.134

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
A

Guanylate kinase

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