SMTL ID : 7vx0.1

The structure of GdmN complex with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: V.44, F.46, H.47, F.103, H.153, H.157, D.176, G.177, R.178, G.207, G.208, Y.210, L.211, E.224, G.325, V.326, H.328, N.329, H.352, D.353 Ligands: FE.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:F.46, A:G.177, A:R.178, A:R.178, A:L.211, A:E.224, A:E.224, A:G.325, A:H.328, A:N.329, A:D.353, A:D.353 Water bridges: A:H.47 Salt bridges: A:H.47, A:H.47, A:H.47, A:H.153, A:H.157 ATP.18: 22 residues within 4Å: Chain B: V.44, F.46, H.47, F.103, H.153, H.157, D.176, G.177, R.178, G.207, G.208, Y.210, L.211, E.224, G.325, V.326, H.328, N.329, H.352, D.353 Ligands: FE.19, EDO.29 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:F.46, B:G.177, B:R.178, B:R.178, B:L.211, B:E.224, B:E.224, B:G.325, B:H.328, B:N.329, B:D.353, B:D.353 Water bridges: B:H.47 Salt bridges: B:H.47, B:H.47, B:H.47, B:H.153, B:H.157

2 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: H.153, H.157, D.176, D.353 Ligands: ATP.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.153, A:H.157, A:D.176, A:D.353 FE.19: 5 residues within 4Å: Chain B: H.153, H.157, D.176, D.353 Ligands: ATP.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.153, B:H.157, B:D.176, B:D.353

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.177, R.178, V.202, S.205, G.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.177, A:S.205

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

SO4.4: 6 residues within 4Å: Chain A: R.438, R.465, R.521, T.552, S.553 Ligands: CP.16 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.469, A:T.552, A:S.553 Water bridges: A:P.437, A:R.465, A:R.465, A:R.521, A:R.521, A:R.521, A:R.521 Salt bridges: A:R.438, A:K.463, A:R.465, A:R.521 SO4.5: 4 residues within 4Å: Chain A: Y.430, G.431, H.442, R.532 7 PLIP interactions: 7 interactions with chain A Water bridges: A:S.382, A:S.382, A:R.532, A:F.533, A:F.533 Salt bridges: A:H.442, A:R.532 SO4.6: 5 residues within 4Å: Chain A: S.169, A.170, H.317, S.318, R.319 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.169, A:S.318, A:S.318, A:R.319 Salt bridges: A:H.317, A:R.319 SO4.7: 3 residues within 4Å: Chain A: R.612, A.622, K.623 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.623 Water bridges: A:R.612, A:R.612 Salt bridges: A:R.612, A:K.623 SO4.20: 5 residues within 4Å: Chain B: R.438, R.469, R.521, T.552, S.553 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.553, B:S.553 Water bridges: B:R.438, B:A.439, B:R.521, B:R.521, B:R.521 Salt bridges: B:R.438, B:R.469, B:R.521 SO4.21: 4 residues within 4Å: Chain B: A.32, R.125, Q.133, R.134 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.35, B:T.35, B:Q.133 Water bridges: B:A.32 Salt bridges: B:R.125, B:R.134 SO4.22: 5 residues within 4Å: Chain B: Y.219, R.279, K.281, G.282, R.465 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.282 Water bridges: B:R.279 Salt bridges: B:R.279, B:R.465

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: L.41, G.42, F.45, L.115, E.118 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: E.66, R.67, P.437, R.438, P.560, I.561 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: A.231, A.294, Q.297, E.298, E.301 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: D.566, D.567, T.684, A.686 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: E.453, T.456, R.457 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: T.544, G.545 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: M.228, G.229, P.232, S.331, V.499, H.515, D.517, T.519 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: L.246, H.258, G.259, N.260, P.269, L.270 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: Q.40, L.41, G.42, F.45, L.115, E.118 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: H.442, G.530, E.531, R.532, F.533 Ligands: PO4.33 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: G.177, V.202, S.205, G.208 Ligands: EDO.27 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: F.45, V.111, H.114 Chain B: M.262, V.263, P.264 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: G.208, N.212, P.264 Ligands: EDO.25 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: H.628, L.629, Y.631, G.634, P.635 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: H.47, D.48, K.73, H.352 Ligands: ATP.18 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: D.34, P.604 Chain B: A.614, G.615, A.618 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain A: L.124 Chain B: R.277, R.280, E.283 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain A: R.121 Chain B: P.635, S.636 Ligand excluded by PLIP

1 x CP: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER(Non-covalent)

CP.16: 10 residues within 4Å: Chain A: K.72, Y.225, K.226, K.463, R.465, R.469, S.553, N.555, N.556 Ligands: SO4.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.463, A:R.465, A:N.555, A:N.555 Water bridges: A:K.226 Salt bridges: A:K.72, A:K.226, A:R.465, A:R.469

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.17: 4 residues within 4Å: Chain A: A.32, R.125, Q.133, R.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.35, A:Q.133 Water bridges: A:A.32 Salt bridges: A:R.125, A:R.134 PO4.33: 5 residues within 4Å: Chain B: Y.430, G.431, H.442, R.532 Ligands: EDO.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.430 Water bridges: B:S.382, B:R.432 Salt bridges: B:H.442, B:R.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, J. et al., Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies. Nat Commun (2022)

Release Date

2022-11-16

Peptides

GdmN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GdmN

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