SMTL ID : 1g1l.2 (1 other biounit)

THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-GLUCOSE COMPLEX.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.62 Chain B: R.62 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.62 Salt bridges: B:R.62, A:R.62 SO4.2: 4 residues within 4Å: Chain A: Q.127, R.128, Q.129, T.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.129, A:T.130 SO4.3: 2 residues within 4Å: Chain A: D.151, Q.152 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.151, A:D.151, A:Q.152, A:Q.152 Water bridges: A:G.153, A:G.153 SO4.4: 4 residues within 4Å: Chain A: H.116 Chain D: L.121, Y.221 Ligands: DAU.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.116 SO4.7: 4 residues within 4Å: Chain B: Q.127, R.128, Q.129, T.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.127, B:Q.129, B:T.130, B:T.130 SO4.10: 6 residues within 4Å: Chain C: S.12, G.13, T.14, R.15, K.25 Ligands: DAU.13 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.13, C:T.14, C:T.14, C:R.15 Water bridges: C:S.12, C:S.12, C:K.25 Salt bridges: C:R.15, C:K.25 SO4.11: 2 residues within 4Å: Chain C: R.128, E.215 7 PLIP interactions: 7 interactions with chain C Water bridges: C:R.128, C:R.128, C:E.215, C:E.215, C:E.215, C:E.215 Salt bridges: C:R.128 SO4.12: 5 residues within 4Å: Chain C: E.160, E.161, R.194, T.200, R.204 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.161 Water bridges: C:R.194, C:R.204, C:R.204, C:R.204 Salt bridges: C:R.194, C:R.204 SO4.15: 5 residues within 4Å: Chain D: S.12, G.13, T.14, R.15, K.25 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.12, D:G.13, D:T.14, D:R.15 Water bridges: D:S.12, D:S.12, D:S.12, D:K.25 Salt bridges: D:R.15, D:K.25 SO4.16: 3 residues within 4Å: Chain C: R.62 Chain D: R.62, Q.65 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:R.62 Salt bridges: D:R.62, C:R.62 SO4.17: 2 residues within 4Å: Chain D: R.128, E.215 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.128, D:R.128 Salt bridges: D:R.128 SO4.18: 4 residues within 4Å: Chain D: E.160, E.161, T.200, R.204 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.161 Water bridges: D:E.160, D:E.161, D:R.204, D:R.204 Salt bridges: D:R.204

8 x DAU: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE(Non-covalent)

DAU.5: 21 residues within 4Å: Chain A: L.8, G.10, G.11, K.25, Q.26, Q.82, P.85, D.86, G.87, L.88, L.108, D.110, N.111, Y.145, G.146, E.161, K.162, V.172, E.196, T.200, W.223 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.88 Hydrogen bonds: A:G.10, A:K.25, A:Q.82, A:Q.82, A:G.87, A:G.109, A:D.110, A:D.110, A:N.111, A:N.111, A:G.146, A:E.161, A:K.162, A:V.172, A:T.200 Water bridges: A:G.11, A:G.11, A:I.199 Salt bridges: A:K.25, A:K.162, A:K.162 DAU.6: 19 residues within 4Å: Chain A: L.45, Y.114, G.115, H.116, D.117, F.118, H.119, E.120, V.250, A.251, E.255, I.256, R.259, Y.293 Chain D: I.216, G.218, R.219, G.220 Ligands: SO4.4 23 PLIP interactions: 15 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:L.45 Hydrogen bonds: A:G.115, A:G.115, A:D.117, A:F.118, A:H.119, A:E.120, A:A.251, D:R.219, D:G.220 Water bridges: A:D.117, A:K.249, A:Y.293, A:Y.293, D:I.216, D:I.216, D:R.219, D:R.219, D:R.219 Salt bridges: A:H.116, A:H.116, A:H.119 pi-Cation interactions: D:R.219 DAU.8: 24 residues within 4Å: Chain B: L.8, A.9, G.10, G.11, K.25, Q.26, Q.82, P.85, D.86, G.87, L.88, L.108, D.110, N.111, Y.145, G.146, E.161, K.162, V.172, G.174, R.194, E.196, T.200, W.223 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:L.88 Hydrogen bonds: B:G.10, B:K.25, B:Q.26, B:Q.82, B:Q.82, B:G.87, B:G.109, B:D.110, B:D.110, B:N.111, B:N.111, B:G.146, B:E.161, B:V.172, B:R.194 Water bridges: B:G.11, B:R.144, B:Y.176, B:Y.176, B:R.194, B:R.194 Salt bridges: B:K.25, B:K.162, B:K.162 DAU.9: 19 residues within 4Å: Chain B: L.45, Y.114, G.115, H.116, D.117, F.118, H.119, E.120, K.249, V.250, A.251, E.255, I.256, R.259, Y.293 Chain C: I.216, G.218, R.219, G.220 24 PLIP interactions: 16 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:L.45 Hydrogen bonds: B:G.115, B:G.115, B:D.117, B:D.117, B:F.118, B:H.119, B:E.120, B:A.251, C:R.219, C:G.220 Water bridges: B:D.117, B:E.120, B:K.249, B:Y.293, C:I.216, C:I.216, C:R.219, C:R.219, C:R.219 Salt bridges: B:H.116, B:H.116, B:H.119 pi-Cation interactions: C:R.219 DAU.13: 26 residues within 4Å: Chain C: L.8, A.9, G.10, G.11, R.15, Q.26, Q.82, P.85, D.86, G.87, L.88, L.108, G.109, D.110, N.111, Y.145, G.146, E.161, K.162, V.172, G.174, Y.176, E.196, T.200, W.223 Ligands: SO4.10 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:L.88 Hydrogen bonds: C:G.10, C:Q.82, C:Q.82, C:G.87, C:G.109, C:D.110, C:D.110, C:N.111, C:N.111, C:G.146, C:E.161, C:V.172, C:T.200 Water bridges: C:G.11, C:G.11, C:E.161, C:K.162, C:Y.176, C:Y.176 Salt bridges: C:R.15, C:K.25, C:K.162, C:K.162 DAU.14: 18 residues within 4Å: Chain B: I.216, G.218, R.219, G.220 Chain C: L.45, Y.114, G.115, H.116, D.117, F.118, H.119, E.120, V.250, A.251, E.255, I.256, R.259, Y.293 21 PLIP interactions: 6 interactions with chain B, 15 interactions with chain C Hydrogen bonds: B:R.219, B:G.220, C:Y.114, C:G.115, C:G.115, C:D.117, C:D.117, C:F.118, C:H.119, C:E.120, C:A.251 Water bridges: B:I.216, B:R.219, B:R.219, C:D.117, C:E.120, C:C.252 pi-Cation interactions: B:R.219 Hydrophobic interactions: C:L.45 Salt bridges: C:H.116, C:H.116 DAU.19: 24 residues within 4Å: Chain D: L.8, A.9, G.10, G.11, Q.26, Q.82, P.85, D.86, G.87, L.88, L.108, G.109, D.110, N.111, Y.145, G.146, E.161, K.162, V.172, G.174, Y.176, E.196, T.200, W.223 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:L.88 Hydrogen bonds: D:G.10, D:R.15, D:Q.82, D:Q.82, D:G.87, D:G.109, D:D.110, D:D.110, D:N.111, D:N.111, D:G.146, D:E.161, D:V.172 Water bridges: D:G.11, D:G.11, D:K.162, D:R.194, D:R.194, D:R.194 Salt bridges: D:K.25, D:K.162, D:K.162 DAU.20: 18 residues within 4Å: Chain A: I.216, G.218, R.219, G.220 Chain D: L.45, Y.114, G.115, H.116, D.117, F.118, H.119, E.120, V.250, A.251, E.255, I.256, R.259, Y.293 21 PLIP interactions: 15 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:L.45 Hydrogen bonds: D:Y.114, D:G.115, D:D.117, D:H.119, D:E.120, D:A.251, A:R.219, A:G.220 Water bridges: D:D.117, D:E.120, D:E.120, D:E.120, D:C.252, A:I.216, A:R.219, A:R.219 Salt bridges: D:H.116, D:H.116, D:H.119 pi-Cation interactions: A:R.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blankenfeldt, W. et al., The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA). EMBO J. (2000)

Release Date

2000-12-27

Peptides

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE

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