SMTL ID : 7vzz.1

The structure of GdmN in complex with the natural tetrahedral intermediate, carbamoyl adenylate, and 20-O-methyl-19-chloroproansamitocin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: E.66, P.437, R.438, S.553, P.560, I.561 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.66, A:R.438, A:S.553, A:S.553, A:I.561 EDO.2: 2 residues within 4Å: Chain A: Q.250, D.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.251 EDO.3: 2 residues within 4Å: Chain A: E.453, R.457 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: K.245, H.258, G.259 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: Q.40, L.41, G.42, L.115, E.118 Ligands: 8CW.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.40, A:G.42 EDO.13: 1 residues within 4Å: Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain A: T.672 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain A: V.60, R.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.432, A:R.432 EDO.16: 6 residues within 4Å: Chain A: Y.225, K.463, R.465, R.469, N.555 Ligands: SO4.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.463, A:R.465, A:R.469, A:R.469, A:S.553 EDO.17: 5 residues within 4Å: Chain B: Y.430, G.431, H.442, E.531, R.532 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.531, B:R.532, B:R.532 EDO.18: 4 residues within 4Å: Chain A: R.611 Chain B: R.607, H.628, D.630 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.611, B:H.628 EDO.19: 3 residues within 4Å: Chain B: K.638, S.640, E.673 No protein-ligand interaction detected (PLIP) EDO.20: 6 residues within 4Å: Chain B: E.66, R.67, P.437, N.555, P.560, I.561 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.66, B:R.67, B:S.553, B:S.553, B:I.561

1 x 8CW: [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl [(~{S})-azanyl-[[(5~{S},6~{E},8~{S},9~{S},12~{R},13~{E},15~{E})-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5-oxidanyl-3,11-bis(oxidanylidene)-2-azabicyclo[16.3.1]docosa-1(21),6,13,15,18(22),19-hexaen-9-yl]oxy]-oxidanyl-methyl] hydrogen phosphate(Non-covalent)

8CW.6: 31 residues within 4Å: Chain A: V.44, F.45, F.46, H.47, F.103, H.107, V.111, H.114, H.153, H.157, D.176, G.177, R.178, G.207, G.208, Y.210, L.211, F.221, E.224, G.324, G.325, V.326, H.328, N.329, H.352, D.353 Chain B: M.262, V.263, P.264 Ligands: EDO.5, FE.12 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.44, A:F.46, A:F.46, A:F.46, A:F.103 Hydrogen bonds: A:H.114, A:D.176, A:D.176, A:G.177, A:R.178, A:L.211, A:E.224, A:G.325, A:N.329, A:D.353, B:M.262 Salt bridges: A:H.47, A:H.157

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

SO4.7: 8 residues within 4Å: Chain A: Y.225, R.438, R.465, R.469, R.521, T.552, S.553 Ligands: EDO.16 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.469, A:S.553, A:S.553 Salt bridges: A:R.438, A:K.463, A:R.465, A:R.521 SO4.8: 4 residues within 4Å: Chain A: Y.430, G.431, H.442, R.532 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.442, A:R.532 SO4.9: 4 residues within 4Å: Chain A: R.612, G.621, A.622, K.623 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.623 Salt bridges: A:R.612, A:K.623 SO4.10: 5 residues within 4Å: Chain A: A.32, T.35, R.125, Q.133, R.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.35, A:T.35, A:Q.133 Salt bridges: A:R.125, A:R.134 SO4.11: 5 residues within 4Å: Chain A: S.169, A.170, H.317, S.318, R.319 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.169, A:S.169, A:S.318, A:S.318, A:R.319 Salt bridges: A:H.317, A:R.319 SO4.21: 6 residues within 4Å: Chain B: Y.225, R.438, R.465, R.521, T.552, S.553 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.553, B:S.553 Salt bridges: B:R.438, B:K.463, B:R.465, B:R.521 SO4.22: 4 residues within 4Å: Chain B: A.32, R.125, Q.133, R.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.35, B:Q.133 Salt bridges: B:R.125, B:R.134

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

FE.12: 5 residues within 4Å: Chain A: H.153, H.157, D.176, D.353 Ligands: 8CW.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.153, A:H.157, A:D.176, A:D.353 FE.23: 5 residues within 4Å: Chain B: H.153, H.157, D.176, D.353 Ligands: CA0.24 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.153, B:H.157, B:D.176, B:D.353

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

CA0.24: 20 residues within 4Å: Chain B: H.47, H.153, H.157, D.176, G.177, R.178, G.207, G.208, Y.210, L.211, E.224, G.324, G.325, V.326, H.328, N.329, H.352, D.353 Ligands: FE.23, 83Z.25 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.177, B:R.178, B:G.207, B:E.224, B:G.325, B:N.329, B:D.353, B:D.353, B:D.353, B:D.353 Salt bridges: B:H.47, B:H.157 pi-Stacking: B:Y.210

1 x 83Z: (5~{S},6~{E},8~{S},9~{S},12~{R},15~{E})-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5,9-bis(oxidanyl)-2-azabicyclo[16.3.1]docosa-1(21),6,15,18(22),19-pentaene-3,11-dione(Non-covalent)

83Z.25: 16 residues within 4Å: Chain A: M.262, V.263, P.264 Chain B: V.44, F.45, F.46, H.47, H.107, V.111, H.114, G.177, R.178, L.211, F.221, D.353 Ligands: CA0.24 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.44, B:F.45, B:F.46, B:F.46 Hydrogen bonds: B:H.47, B:H.107, A:M.262

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

Related Entries With Identical Sequence