4V5B

Structure of PDF binding helix in complex with the ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.323
  • R-Value Work: 0.259

Literature

Macromolecules
Sequence Display for 4V5B

Classification: RIBOSOME

Total Structure Weight: 4295349.00


Macromolecule Entities
Molecule Chains Length Organism Details
50S RIBOSOMAL PROTEIN L32 A0, C0 56 Escherichia coli Gene Name(s): rpmF b1089 JW1075
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L33 A1, C1 54 Escherichia coli Fragment: RESIDUES 2-55
Gene Name(s): rpmG b3636 JW3611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L34 A2, C2 46 Escherichia coli Gene Name(s): rpmH rimA ssaF b3703 JW3680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L35 A3, C3 64 Escherichia coli Fragment: RESIDUES 2-65
Gene Name(s): rpmI b1717 JW1707
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L36 A4, C4 38 Escherichia coli Gene Name(s): rpmJ b3299 JW3261
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
C-TERM HELIX PDF A5 16 Escherichia coli EC#: 3.5.1.88 IUBMB
Mutation: L146A
Gene Name(s): def fms b3287 JW3248
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L2 AC, CC 273 Escherichia coli Gene Name(s): rplB b3317 JW3279
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L3 AD, CD 209 Escherichia coli Gene Name(s): rplC b3320 JW3282
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L4 AE, CE 201 Escherichia coli Gene Name(s): rplD eryA b3319 JW3281
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L5 AF, CF 178 Escherichia coli Fragment: RESIDUES 2-179
Gene Name(s): rplE b3308 JW3270
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L6 AG, CG 176 Escherichia coli Fragment: RESIDUES 2-177
Gene Name(s): rplF b3305 JW3267
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L9 AH, CH 149 Escherichia coli Gene Name(s): rplI b4203 JW4161
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L11 AI, CI 141 Escherichia coli Fragment: RESIDUES 2-142
Gene Name(s): rplK relC b3983 JW3946
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L13 AJ, CJ 142 Escherichia coli Gene Name(s): rplM b3231 JW3200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L14 AK, CK 123 Escherichia coli Gene Name(s): rplN b3310 JW3272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L15 AL, CL 144 Escherichia coli Gene Name(s): rplO b3301 JW3263
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L16 AM, CM 136 Escherichia coli Gene Name(s): rplP b3313 JW3275
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L17 AN, CN 127 Escherichia coli Gene Name(s): rplQ b3294 JW3256
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L18 AO, CO 117 Escherichia coli Fragment: RESIDUES 2-57
Gene Name(s): rplR b3304 JW3266
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L19 AP, CP 114 Escherichia coli Fragment: RESIDUES 2-115
Gene Name(s): rplS b2606 JW2587
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L20 AQ, CQ 117 Escherichia coli Fragment: RESIDUES 2-118
Gene Name(s): rplT pdzA b1716 JW1706
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L21 AR, CR 103 Escherichia coli Gene Name(s): rplU b3186 JW3153
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L22 AS, CS 110 Escherichia coli Gene Name(s): rplV eryB b3315 JW3277
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L23 AT, CT 100 Escherichia coli Gene Name(s): rplW b3318 JW3280
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24 AU, CU 103 Escherichia coli Fragment: RESIDUES 2-104
Gene Name(s): rplX b3309 JW3271
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L25 AV, CV 94 Escherichia coli Gene Name(s): rplY b2185 JW2173
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L27 AW, CW 84 Escherichia coli Fragment: RESIDUES 2-85
Gene Name(s): rpmA b3185 JW3152
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L29 AX, CX 63 Escherichia coli Gene Name(s): rpmC b3312 JW3274
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L30 AY, CY 58 Escherichia coli Fragment: RESIDUES 2-59
Gene Name(s): rpmD b3302 JW3264
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L31 AZ, CZ 70 Escherichia coli Gene Name(s): rpmE b3936 JW3907
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S2 BB, DB 240 Escherichia coli Fragment: RESIDUES 2-241
Gene Name(s): rpsB c0204
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S3 BC, DC 232 Escherichia coli Fragment: RESIDUES 2-233
Gene Name(s): rpsC c4080
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S4 BD, DD 205 Escherichia coli Fragment: RESIDUES 2-206
Gene Name(s): rpsD ramA b3296 JW3258
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S5 BE, DE 166 Escherichia coli Fragment: RESIDUES 2-167
Gene Name(s): rpsE spc b3303 JW3265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S6 BF, DF 135 Escherichia coli Gene Name(s): rpsF b4200 JW4158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S7 BG, DG 178 Escherichia coli Fragment: RESIDUES 2-156
Gene Name(s): rpsG b3341 JW3303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S8 BH, DH 129 Escherichia coli Fragment: RESIDUES 2-130
Gene Name(s): rpsH b3306 JW3268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S9 BI, DI 129 Escherichia coli Fragment: RESIDUES 2-130
Gene Name(s): rpsI c3984
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S10 BJ, DJ 103 Escherichia coli Gene Name(s): rpsJ nusE c4092
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S11 BK, DK 128 Escherichia coli Fragment: RESIDUES 2-129
Gene Name(s): rpsK b3297 JW3259
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S12 BL, DL 123 Escherichia coli Fragment: RESIDUES 2-124
Gene Name(s): rpsL strA c4116
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S13 BM, DM 117 Escherichia coli Fragment: RESIDUES 2-118
Gene Name(s): rpsM Z4668 ECs4163
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S14 BN, DN 100 Escherichia coli Fragment: RESIDUES 2-101
Gene Name(s): rpsN b3307 JW3269
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S15 BO, DO 89 Escherichia coli Gene Name(s): rpsO secC b3165 JW3134
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S16 BP, DP 82 Escherichia coli Gene Name(s): rpsP b2609 JW2590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S17 BQ, DQ 83 Escherichia coli Fragment: RESIDUES 2-84
Gene Name(s): rpsQ neaA b3311 JW3273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S18 BR, DR 74 Escherichia coli Fragment: RESIDUES 2-75
Gene Name(s): rpsR Z5811 ECs5178
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S19 BS, DS 91 Escherichia coli Fragment: RESIDUES 2-92
Gene Name(s): rpsS b3316 JW3278
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S20 BT, DT 86 Escherichia coli Fragment: RESIDUES 2-87
Gene Name(s): rpsT b0023 JW0022
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S RIBOSOMAL PROTEIN S21 BU, DU 71 Escherichia coli Gene Name(s): rpsU c3816
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5S RIBOSOMAL RNA AA, CA 120 Escherichia coli
23S RIBOSOMAL RNA AB, CB 2904 Escherichia coli
16S RIBOSOMAL RNA BA, DA 1542 Escherichia coli

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

AB, AE, BA, BN, BT, CB, CC, CL, DA, DN MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.323
  • R-Value Work: 0.259
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 208.18 α = 90.00
b = 380.08 β = 90.00
c = 736.70 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2007-11-22
  • Released Date: 2014-07-09
  • Deposition author(s): Bingel-Erlenmeyer, R., Kohler, R., Kramer, G., Sandikci, A., Antolic, S., Maier, T., Schaffitzel, C., Wiedmann, B., Bukau, B., Ban, N.
  • Previous versions: 2VHM 2VHN 2VHO 2VHP

Revision History

  • Version 1_0: 2014-07-09

    Type: Initial release

  • Version 1_1: 2014-12-10

    Type: Other