SMTL ID : 1g3l.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.128, E.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.215 Salt bridges: A:R.128 SO4.4: 3 residues within 4Å: Chain A: R.62 Chain B: P.61, R.62 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.62, B:R.62 SO4.5: 2 residues within 4Å: Chain B: R.128, E.215 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.128 SO4.8: 3 residues within 4Å: Chain C: R.128, Q.129, T.130 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.129, C:T.130, C:T.130 SO4.11: 3 residues within 4Å: Chain D: R.128, Q.129, T.130 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.129, D:T.130

8 x TRH: 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE(Non-covalent)

TRH.2: 24 residues within 4Å: Chain A: L.8, A.9, G.10, G.11, Q.82, P.85, D.86, G.87, L.108, D.110, R.144, Y.145, G.146, E.161, K.162, V.172, T.173, G.174, Y.176, R.194, E.196, I.199, T.200, W.223 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.108, A:W.223 Hydrogen bonds: A:G.10, A:Q.82, A:Q.82, A:G.87, A:D.110, A:G.146, A:E.161, A:K.162, A:Y.176, A:T.200 Salt bridges: A:K.162, A:K.162, A:R.194 TRH.3: 18 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 C: I.216, G.218, R.219, G.220 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.45, C:I.216 Hydrogen bonds: A:Y.114, A:G.115, A:H.116, A:D.117, A:H.119, A:E.120, A:A.251, C:R.219, C:G.220 Salt bridges: A:H.116, A:H.116 pi-Cation interactions: C:R.219 TRH.6: 24 residues within 4Å: Chain B: L.8, A.9, G.10, G.11, K.25, Q.82, P.85, D.86, G.87, L.88, L.108, D.110, R.144, Y.145, G.146, E.161, K.162, V.172, T.173, G.174, Y.176, R.194, E.196, T.200 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.88, B:L.108, B:Y.145 Hydrogen bonds: B:G.10, B:K.25, B:Q.82, B:Q.82, B:G.87, B:D.110, B:G.146, B:K.162, B:T.200 Salt bridges: B:K.162, B:K.162, B:R.194 TRH.7: 17 residues within 4Å: Chain B: 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: G.218, R.219, G.220 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:L.45 Hydrogen bonds: B:G.115, B:H.116, B:D.117, B:D.117, B:H.119, B:E.120, B:E.120, B:A.251, D:R.219, D:R.219, D:G.220 Salt bridges: B:H.116, B:H.116 pi-Cation interactions: D:R.219 TRH.9: 22 residues within 4Å: Chain C: L.8, G.10, G.11, Q.26, Q.82, P.85, D.86, G.87, L.108, D.110, R.144, Y.145, G.146, E.161, K.162, V.172, T.173, Y.176, R.194, E.196, I.199, T.200 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:P.85, C:L.108 Hydrogen bonds: C:G.10, C:G.11, C:Q.82, C:Q.82, C:G.87, C:D.110, C:G.146, C:E.161, C:K.162, C:Y.176 Salt bridges: C:K.162, C:K.162, C:K.162, C:R.194 TRH.10: 17 residues within 4Å: Chain A: 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 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain C Hydrogen bonds: A:G.220, C:G.115, C:H.116, C:D.117, C:D.117, C:F.118, C:H.119, C:E.120, C:K.249, C:A.251 pi-Cation interactions: A:R.219 Hydrophobic interactions: C:L.45 Salt bridges: C:H.116, C:H.116 TRH.12: 25 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, D.110, Y.145, G.146, E.161, K.162, V.172, T.173, G.174, Y.176, R.194, E.196, I.199, T.200, W.223 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:L.88, D:L.108, D:Y.145, D:W.223 Hydrogen bonds: D:G.10, D:Q.82, D:Q.82, D:G.87, D:D.110, D:G.146, D:K.162, D:K.162, D:T.200, D:T.200 Salt bridges: D:K.162, D:K.162, D:K.162, D:R.194 TRH.13: 18 residues within 4Å: Chain B: 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 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:L.45, B:I.216 Hydrogen bonds: D:G.115, D:G.115, D:H.116, D:D.117, D:F.118, D:H.119, D:E.120, D:E.120, D:A.251, B:G.220 Salt bridges: D:H.116, D:H.116 pi-Cation interactions: B: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
A

B
B

C
C

D
D

GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE

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