SMTL ID : 7vzq.1

The structure of GdmN V24Y/G157A/R158A/G188R mutant in complex with carbamoyl adenylate intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

CP.1: 6 residues within 4Å: Chain A: Y.430, G.431, H.442, G.530, E.531, R.532 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.442, A:E.531, A:R.532 Water bridges: A:R.432, A:H.442, A:F.533, A:F.533, A:F.533 Salt bridges: A:H.442, A:R.532

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: CA0.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.153, A:H.157, A:D.176, A:D.353 FE.13: 5 residues within 4Å: Chain B: H.153, H.157, D.176, D.353 Ligands: CA0.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.153, B:H.157, B:D.176, B:D.353

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

EDO.3: 8 residues within 4Å: Chain A: P.349, A.381, E.434, F.435, G.436, P.437, R.438, L.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.436, A:R.438 EDO.4: 6 residues within 4Å: Chain A: Q.392, A.395, R.396, D.399, D.690, I.691 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.392 EDO.5: 4 residues within 4Å: Chain A: V.149, Y.150, P.152, E.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.150, A:E.155 EDO.6: 2 residues within 4Å: Chain A: S.564, D.567 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.564, A:D.567 EDO.14: 9 residues within 4Å: Chain B: P.349, A.381, E.434, F.435, G.436, P.437, R.438, L.440, F.495 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.349, B:R.438 EDO.15: 6 residues within 4Å: Chain B: M.228, A.231, P.232, Q.297, E.301, S.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.331, B:S.331

2 x CA0: 5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine(Non-covalent)

CA0.7: 18 residues within 4Å: Chain A: H.47, H.157, D.176, A.177, A.178, G.207, R.208, Y.210, L.211, E.224, Y.225, G.325, V.326, H.328, N.329, H.352, D.353 Ligands: FE.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.177, A:A.178, A:A.178, A:G.207, A:E.224, A:G.325, A:H.328, A:N.329, A:D.353 Salt bridges: A:H.47, A:H.157 CA0.16: 20 residues within 4Å: Chain B: H.47, H.153, H.157, D.176, A.177, A.178, G.207, R.208, Y.210, L.211, E.224, Y.225, M.228, G.325, V.326, H.328, N.329, H.352, D.353 Ligands: FE.13 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.177, B:A.178, B:A.178, B:G.207, B:L.211, B:E.224, B:G.325, B:N.329, B:D.353, B:D.353 Salt bridges: B:H.47, B:H.157

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

SO4.8: 6 residues within 4Å: Chain A: Y.225, R.438, R.465, R.521, T.552, S.553 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.552, A:S.553 Water bridges: A:R.438, A:A.439, A:R.465, A:R.465, A:R.521, A:R.521, A:R.521 Salt bridges: A:R.438, A:K.463, A:R.465, A:R.521 SO4.9: 5 residues within 4Å: Chain A: K.72, Y.225, K.226, R.465, R.469 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.225 Salt bridges: A:K.72, A:K.226, A:R.465, A:R.469 SO4.10: 4 residues within 4Å: Chain A: R.612, G.621, A.622, K.623 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.623 Salt bridges: A:R.612 SO4.11: 5 residues within 4Å: Chain A: A.32, T.35, R.125, Q.133, R.134 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.35, A:T.35, A:Q.133 Water bridges: A:A.32 Salt bridges: A:R.125, A:R.134 SO4.12: 5 residues within 4Å: Chain A: S.169, A.170, H.317, S.318, R.319 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.169, A:S.318, A:S.318, A:R.319 Water bridges: A:S.318, A:S.318 Salt bridges: A:H.317, A:R.319 SO4.17: 5 residues within 4Å: Chain B: R.438, R.465, R.521, T.552, S.553 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.552, B:S.553 Water bridges: B:A.439, B:R.521, B:R.521 Salt bridges: B:R.438, B:R.465, B:R.521 SO4.18: 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 SO4.19: 3 residues within 4Å: Chain B: R.279, K.281, G.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.282 Salt bridges: B:R.279, B:K.281

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 2 residues within 4Å: Chain B: H.442, R.532 Ligand excluded by PLIP

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