SMTL ID : 5m8h.1

ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-4-4-mer

Ligands

10 x SR: STRONTIUM ION(Non-functional Binders)

SR.1: 3 residues within 4Å: Chain A: D.77, T.79, S.309 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.77, A:D.77, A:T.79, H2O.4 SR.2: 2 residues within 4Å: Chain A: N.145, D.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:N.145, A:D.148 SR.8: 2 residues within 4Å: Chain B: N.145, D.148 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:N.145, B:D.148 SR.9: 3 residues within 4Å: Chain B: D.77, T.79, S.309 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.77, B:T.79, H2O.6 SR.16: 1 residues within 4Å: Chain C: Q.382 No protein-ligand interaction detected (PLIP) SR.17: 2 residues within 4Å: Chain C: N.145, D.148 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:N.145, C:D.148, H2O.13 SR.18: 3 residues within 4Å: Chain C: D.77, T.79, S.309 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.77, C:T.79 SR.22: 2 residues within 4Å: Chain D: Q.194, Q.197 No protein-ligand interaction detected (PLIP) SR.23: 3 residues within 4Å: Chain D: D.77, T.79, S.309 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.79, H2O.16 SR.24: 2 residues within 4Å: Chain D: N.145, D.148 No protein-ligand interaction detected (PLIP)

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

CL.3: 4 residues within 4Å: Chain A: D.9, V.10, L.11, D.14 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: D.380 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: G.110, L.111, T.280, Q.281 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: Q.382 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: G.126, Q.304 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: R.384, L.385 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain D: I.144, L.153 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain E: D.180, T.181, G.182, T.184 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain E: K.58, L.59, I.60 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain E: G.182, R.186, A.192 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain F: L.128, L.174, R.193 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain F: R.186, E.191, A.192 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain G: R.186, A.192 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain H: R.186, E.191, A.192 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain H: D.180, T.181, G.182, T.184 Ligand excluded by PLIP

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 4 residues within 4Å: Chain A: E.128, E.238, R.288, Q.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.238 MPD.6: 11 residues within 4Å: Chain A: D.133, L.136, I.137, I.270, F.272, G.286, G.287, R.288, T.306, G.307, F.308 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.136, A:I.270, A:F.308 Hydrogen bonds: A:D.133 MPD.7: 8 residues within 4Å: Chain A: H.105, P.117, Q.119, L.283, R.285, S.309, M.310, D.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.119, A:R.285, A:D.311 Hydrogen bonds: A:Q.119 MPD.13: 7 residues within 4Å: Chain B: P.117, Q.119, L.283, R.285, S.309, M.310, D.311 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.119, B:R.285, B:D.311 Hydrogen bonds: B:Q.119 MPD.14: 6 residues within 4Å: Chain B: E.260, S.262, Y.275, R.285 Chain F: Y.106, Q.207 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:E.260, B:S.262, B:R.285, F:Q.207 MPD.15: 7 residues within 4Å: Chain B: V.20, L.21, S.146, L.147, D.148, Q.320, L.321 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.20, B:L.21, B:D.148 MPD.20: 6 residues within 4Å: Chain C: E.260, S.262, P.282, R.285 Chain H: Y.106, Q.207 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.262, C:S.262 MPD.21: 8 residues within 4Å: Chain C: P.117, Q.119, P.282, L.283, R.285, S.309, M.310, D.311 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:P.117, C:D.311 Hydrogen bonds: C:Q.119 Water bridges: C:R.285, C:S.309, C:S.309, C:S.309 MPD.26: 8 residues within 4Å: Chain D: V.103, H.105, P.117, Q.119, L.283, S.309, M.310, D.311 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.103, D:P.117, D:Q.119 Hydrogen bonds: D:Q.119 MPD.27: 2 residues within 4Å: Chain D: Q.355, Y.357 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.357 MPD.31: 6 residues within 4Å: Chain D: E.260, S.262, Y.275, P.282 Chain E: Q.207, K.211 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.262, D:S.262 MPD.35: 4 residues within 4Å: Chain A: A.185, E.260, S.262 Chain G: Q.207 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stroek, R. et al., Kinetics and Structure of a Cold-Adapted Hetero-Octameric ATP Phosphoribosyltransferase. Biochemistry (2017)

Release Date

2017-09-06

Peptides

ATP phosphoribosyltransferase regulatory subunit: ABCD
ATP phosphoribosyltransferase: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

ATP phosphoribosyltransferase regulatory subunit

ATP phosphoribosyltransferase

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