SMTL ID : 1kjq.1

Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.266, E.278 Ligands: ADP.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.266, A:E.278, H2O.78, H2O.434 MG.2: 2 residues within 4Å: Chain B: E.278 Ligands: ADP.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.278, H2O.642, H2O.939

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: A.52, H.53 Chain B: M.49, H.50, A.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.49 NA.4: 4 residues within 4Å: Chain A: N.99, V.100, P.102, C.103 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.99, A:V.100 Water bridges: A:V.100, A:Y.260, A:Y.260

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

CL.5: 3 residues within 4Å: Chain A: R.118, R.132, F.133 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.42, N.59 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: H.215, F.216 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: T.5 Chain B: F.336, L.351, F.352, G.353 Ligand excluded by PLIP

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

ADP.9: 17 residues within 4Å: Chain A: R.113, S.129, I.152, K.154, Q.164, E.194, G.195, V.196, V.197, F.199, E.202, Q.224, E.266, F.268, S.277, E.278 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.129, A:K.154, A:Q.164, A:E.194, A:E.194, A:V.197, A:E.202, A:E.278 Water bridges: A:R.113, A:Q.224, A:E.266, A:S.277, A:S.277, A:E.278, A:E.278 Salt bridges: A:R.113, A:R.113, A:K.154 ADP.10: 15 residues within 4Å: Chain B: R.113, S.129, I.152, K.154, Q.164, E.194, G.195, V.196, V.197, F.199, E.202, Q.224, F.268, E.278 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.129, B:K.154, B:Q.164, B:E.194, B:E.194, B:V.197, B:E.202, B:E.278 Water bridges: B:R.113, B:R.113, B:Q.224, B:S.277, B:E.278 Salt bridges: B:R.113, B:R.113, B:K.154

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.11: 7 residues within 4Å: Chain A: D.45, M.49, H.50, R.54, S.55 Chain B: L.7, H.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.55, A:S.55 Water bridges: A:H.53, A:S.55 Salt bridges: A:D.45

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

EDO.12: 6 residues within 4Å: Chain A: L.33, R.304, L.309 Chain B: V.343, Q.348, I.349 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.349, B:I.349, A:R.304 Water bridges: B:R.350, A:R.304 EDO.13: 7 residues within 4Å: Chain B: E.29, R.32, D.295, L.296, S.297, A.300 Ligands: EDO.25 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.32, B:S.297 Water bridges: A:R.32 EDO.14: 3 residues within 4Å: Chain A: W.233, V.373, I.377 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.236 EDO.15: 6 residues within 4Å: Chain B: G.20, E.21, L.22, G.23, E.81, R.362 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.20, B:E.21, B:E.21, B:L.22, B:G.23, B:R.362 Water bridges: B:K.354 EDO.16: 3 residues within 4Å: Chain A: R.245, E.273, V.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.274 EDO.17: 1 residues within 4Å: Chain A: R.68 No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain A: T.1, L.2, Y.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.2 EDO.19: 2 residues within 4Å: Chain B: Q.328, L.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.328 Water bridges: B:Q.328, B:Q.328 EDO.20: 2 residues within 4Å: Chain A: N.59, D.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.59, A:D.62, A:D.62 EDO.21: 3 residues within 4Å: Chain A: E.378, R.379, H.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.378, A:E.378 Water bridges: A:R.379 EDO.22: 3 residues within 4Å: Chain A: R.223, R.230, V.324 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.223, A:R.230 Water bridges: A:V.324, A:L.326 EDO.23: 5 residues within 4Å: Chain B: F.133, A.134, L.139, E.142, A.143 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.139 Water bridges: B:E.142 EDO.24: 3 residues within 4Å: Chain B: L.243, E.244, Q.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.247 Water bridges: B:E.244 EDO.25: 6 residues within 4Å: Chain A: L.291, I.292, Q.348, R.350 Chain B: D.295 Ligands: EDO.13 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.348, A:R.350 Water bridges: A:L.291, A:L.291, A:R.350, B:R.32, B:R.32, B:Y.317 EDO.26: 5 residues within 4Å: Chain A: G.63, A.86, D.88, M.89, Q.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.86, A:M.89, A:Q.92 Water bridges: A:G.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. J.Biol.Chem. (2002)

Release Date

2002-06-28

Peptides

phosphoribosylglycinamide formyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

phosphoribosylglycinamide formyltransferase 2

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