SMTL ID : 1fxo.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.128, E.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.215 Water bridges: A:R.128 Salt bridges: A:R.128 SO4.2: 4 residues within 4Å: Chain C: Q.127, 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 SO4.3: 2 residues within 4Å: Chain C: R.62 Chain D: R.62 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Water bridges: D:A.22, C:R.62, C:R.62, C:R.62 Salt bridges: D:R.62, C:R.62 SO4.4: 2 residues within 4Å: Chain C: D.151, Q.152 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.152 Water bridges: C:Q.152, C:Q.152, C:G.153 SO4.5: 4 residues within 4Å: Chain D: Q.127, R.128, Q.129, T.130 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.129, D:T.130 SO4.6: 4 residues within 4Å: Chain B: R.245 Chain D: R.144, D.225, S.231 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain B Water bridges: D:D.141, D:R.144, D:S.231, D:S.231, B:R.245 Salt bridges: D:R.144, B:R.245 SO4.7: 2 residues within 4Å: Chain D: D.151, Q.152 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.152 Water bridges: D:G.153 SO4.8: 2 residues within 4Å: Chain D: K.2, R.49 3 PLIP interactions: 3 interactions with chain D Water bridges: D:G.47, D:R.49 Salt bridges: D:K.2

8 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.9: 14 residues within 4Å: Chain A: L.8, A.9, G.10, G.11, K.25, Q.26, Q.82, P.85, D.86, G.87, L.88, G.109, D.110, E.196 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.88 Hydrogen bonds: A:G.10, A:Q.26, A:Q.82, A:Q.82, A:G.87, A:G.109, A:D.110, A:D.110 Water bridges: A:G.11, A:K.25, A:K.25, A:K.25 Salt bridges: A:K.25 TMP.10: 14 residues within 4Å: Chain B: 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, E.196 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.88 Hydrogen bonds: B:G.10, B:Q.26, B:Q.82, B:Q.82, B:G.87, B:G.109, B:D.110, B:D.110 Water bridges: B:G.11, B:S.12, B:K.25, B:R.144 Salt bridges: B:K.25, B:K.162 TMP.11: 13 residues within 4Å: Chain C: L.8, G.10, G.11, K.25, Q.26, Q.82, P.85, D.86, G.87, L.88, G.109, D.110, E.196 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.88 Hydrogen bonds: C:G.10, C:Q.26, C:Q.82, C:Q.82, C:G.87, C:G.109, C:D.110, C:D.110 Water bridges: C:G.11, C:R.144, C:D.225 Salt bridges: C:K.25, C:K.162 TMP.12: 12 residues within 4Å: Chain D: L.8, G.10, G.11, Q.26, Q.82, P.85, D.86, G.87, L.88, G.109, D.110, E.196 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.88 Hydrogen bonds: D:G.10, D:Q.26, D:Q.82, D:Q.82, D:G.87, D:G.109, D:D.110, D:D.110 Water bridges: D:G.11, D:G.11, D:R.15, D:R.15, D:K.162, D:G.227 TMP.13: 14 residues within 4Å: Chain A: L.45, Y.114, G.115, H.116, D.117, F.118, V.250, A.251, E.255, I.256, R.259 Chain C: G.218, R.219, G.220 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.45 Hydrogen bonds: A:G.115, A:G.115, A:D.117, A:A.251, C:R.219, C:R.219, C:R.219, C:G.220 Water bridges: A:D.117, A:D.117, A:C.252, A:E.255, A:Y.293 Salt bridges: A:H.116 pi-Cation interactions: C:R.219 TMP.14: 14 residues within 4Å: Chain B: L.45, Y.114, G.115, H.116, D.117, F.118, V.250, A.251, E.255, I.256, R.259 Chain D: G.218, R.219, G.220 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:L.45 Hydrogen bonds: B:G.115, B:G.115, B:D.117, B:A.251, D:R.219, D:R.219, D:R.219, D:G.220 Water bridges: B:S.41, B:D.117, B:C.252, B:E.255, B:Y.293 Salt bridges: B:H.116 pi-Cation interactions: D:R.219 TMP.15: 14 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, V.250, A.251, E.255, I.256, R.259 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:L.45 Hydrogen bonds: C:Y.114, C:G.115, C:D.117, C:A.251, A:R.219, A:R.219, A:G.220 Water bridges: C:H.116, C:H.119, C:H.119, C:K.249, C:C.252, C:Y.293, A:R.219, A:R.219 Salt bridges: C:H.116 pi-Cation interactions: A:R.219 TMP.16: 14 residues within 4Å: Chain B: G.218, R.219, G.220 Chain D: L.45, Y.114, G.115, H.116, D.117, F.118, V.250, A.251, E.255, I.256, R.259 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.45 Hydrogen bonds: D:Y.114, D:G.115, D:D.117, D:A.251, B:R.219, B:R.219, B:G.220 Water bridges: D:D.117, D:H.119, D:K.249, D:E.255, D:Y.293, B:R.219, B:R.219 Salt bridges: 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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