SMTL ID : 7vzy.1

The structure of GdmN complex with AMP and 20-O-methyl-19-chloroproansamitocin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

2 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.1: 17 residues within 4Å: Chain A: V.44, F.45, F.46, H.47, H.107, V.111, H.114, G.177, R.178, L.211, F.221, D.353 Chain B: M.262, V.263, P.264 Ligands: AMP.3, EDO.11 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.44, A:F.45, A:F.46, A:R.178 Hydrogen bonds: A:H.107, A:G.177, A:R.178, A:R.178, A:D.353, B:M.262 83Z.17: 18 residues within 4Å: Chain A: M.262, V.263, P.264 Chain B: V.44, F.45, F.46, H.47, Y.102, F.103, H.107, V.111, H.114, G.177, R.178, L.211, F.221, D.353 Ligands: AMP.19 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.44, B:F.46, B:F.46, B:F.46, B:F.103, B:R.178 Hydrogen bonds: B:H.107, B:R.178, B:D.353, A:M.262

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: AMP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.153, A:H.157, A:D.176, A:D.353, AMP.3 FE.18: 5 residues within 4Å: Chain B: H.153, H.157, D.176, D.353 Ligands: AMP.19 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.153, B:H.157, B:D.176, B:D.353, AMP.19

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 18 residues within 4Å: Chain A: H.47, H.157, D.176, G.177, 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: 83Z.1, FE.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.211, A:E.224, A:E.224, A:G.325, A:H.328, A:N.329, A:D.353, A:D.353 Salt bridges: A:H.47, A:H.157 AMP.19: 18 residues within 4Å: Chain B: H.47, H.157, D.176, G.177, 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: 83Z.17, FE.18 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.224, B:G.325, B:H.328, B:N.329, B:D.353, B:D.353 Salt bridges: B:H.47, B:H.157 pi-Stacking: B:Y.210

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: E.66, K.72, P.437, P.560, I.561 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.67, A:P.437, A:I.561

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

SO4.5: 8 residues within 4Å: Chain A: Y.225, R.438, R.465, R.469, R.521, T.552, S.553 Ligands: CP.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.469, A:T.552, A:S.553 Salt bridges: A:R.438, A:K.463, A:R.465, A:R.521 SO4.6: 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 SO4.7: 5 residues within 4Å: Chain A: A.32, T.35, R.125, Q.133, R.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.35, A:Q.133 Salt bridges: A:R.125, A:R.134 SO4.8: 4 residues within 4Å: Chain A: S.169, 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 SO4.9: 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 SO4.20: 5 residues within 4Å: Chain B: R.438, R.469, R.521, T.552, S.553 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.469, B:S.553, B:S.553 Salt bridges: B:R.438, B:K.463, B:R.521 SO4.21: 4 residues within 4Å: Chain B: A.32, R.125, Q.133, R.134 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.35, B:T.35, B:Q.133 Salt bridges: B:R.125, B:R.134

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

CP.10: 9 residues within 4Å: Chain A: K.72, Y.225, K.226, K.463, R.465, R.469, S.553, N.555 Ligands: SO4.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.72, A:Y.225, A:K.226, A:K.226, A:R.469, A:N.555 Salt bridges: A:K.72, A:K.463, A:R.465, A:R.469

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

EDO.11: 6 residues within 4Å: Chain A: Q.40, L.41, G.42, F.45, L.115 Ligands: 83Z.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.40, A:G.42 EDO.12: 5 residues within 4Å: Chain A: K.245, L.246, H.258, G.259, N.260 No protein-ligand interaction detected (PLIP) EDO.13: 10 residues within 4Å: Chain A: H.328, P.349, A.381, E.434, F.435, G.436, P.437, R.438, L.440, F.495 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.438 EDO.14: 7 residues within 4Å: Chain A: R.67, L.68, R.70, Q.563, S.564, D.567 Ligands: PEG.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.70, A:D.567 EDO.15: 4 residues within 4Å: Chain A: G.389, R.390, E.391, Q.392 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.390, A:E.391, A:Q.392, A:Q.392 EDO.22: 4 residues within 4Å: Chain B: E.66, P.437, P.560, I.561 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.66, B:I.561

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 9 residues within 4Å: Chain A: S.564, D.566, D.567, T.570, W.678, T.684, L.685, A.686 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.564, A:T.570, A:L.683, A:L.685

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