Research workbench
Structure of the phycobilisome from the red alga Porphyridium purpureum
Analyse Structure of the phycobilisome from the red alga Porphyridium purpureum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KGX
- Type
- protein
- Length
- 125,515 residues
- Chains
- 706
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Porphyridium purpureum
- Molecule
- Phycoerythrin alpha subunit; B-phycoerythrin beta chain; LR7; LR2_Hb; LR9; LR1; LR4…
- UniProt
- E2IH77, P11393, W0RZ90, W0RYI4, W0RZB2, W0RYM0, W0S279, W0S1U6, W0RZE2, W0RZJ2
- Ligands
- PEB, CYC, PUB
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · resolution 2.8 · 32 distinct chains · 45% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A1, C1, E1, G1, I1, K1, N1, P1, R1, T1, V1, X1, c1, e1, g1, i1, k1, m1, p1, r1, t1, v1, x1, z1, O2, Q2, S2, U2, W2, Z2, b2, d2, f2, h2, j2, l2, A3, C3, E3, G3, I3, K3, M3, O3, Q3, S3, U3, W3, A4, C4, E4, G4, I4, K4, N4, P4, R4, T4, V4, X4, c4, e4, g4, i4, k4, m4, p4, r4, t4, v4, x4, z4, J5, O6, Q6, S6, U6, W6, Z6, b6, d6, f6, h6, j6, l6, O7, Q7, S7, U7, W7, Z7, b7, d7, f7, h7, j7, l7, C8, E8, G8, I8, K8, M8, O8, Q8, S8, U8, W8, Y8, a8, d8, f8, h8, j8, l8, B9, D9, F9, H9, J9, L9, N9, P9, R9, T9, V9, X9, CA, EA, GA, IA, KA, MA, OA, QA, SA, UA, WA, YA, aA, dA, fA, hA, jA, lA, OB, QB, SB, UB, WB, ZB, bB, dB, fB, hB, jB, lB, JC, AD, CD, ED, GD, ID, KD, MD, OD, QD, SD, UD, WD, AE, CE, EE, GE, IE, KE, ME, OE, QE, SE, UE, WE, YE, aE, cE, eE, gE, iE, kE, mE, oE, qE, sE, uE, OF, QF, SF, UF, WF, ZF, bF, dF, fF, hF, jF, lF, AG, CG, EG, GG, IG, KG, MG, OG, QG, SG, UG, WG, YG, aG, cG, eG, gG, iG, kG, mG, oG, qG, sG, uG, OI, QI, SI, UI, WI, ZI, bI, dI, fI, hI, jI, lI, BJ, DJ, FJ, HJ, JJ, LJ, NJ, PJ, RJ, TJ, VJ, XJ | Phycoerythrin alpha subunit | protein | 164 | 45% helix, 0% strand | E2IH77 |
| B1, D1, F1, H1, J1, L1, O1, Q1, S1, U1, W1, Y1, d1, f1, h1, j1, l1, n1, q1, s1, u1, w1, y1, 11, P2, R2, T2, V2, Y2, a2, c2, e2, g2, i2, k2, m2, B3, D3, F3, H3, J3, L3, N3, P3, R3, T3, V3, X3, B4, D4, F4, H4, J4, L4, O4, Q4, S4, U4, W4, Y4, d4, f4, h4, j4, l4, n4, q4, s4, u4, w4, y4, 14, I5, K5, P6, R6, T6, V6, Y6, a6, c6, e6, g6, i6, k6, m6, P7, R7, T7, V7, Y7, a7, c7, e7, g7, i7, k7, m7, D8, F8, H8, J8, L8, N8, P8, R8, T8, V8, X8, Z8, c8, e8, g8, i8, k8, m8, C9, E9, G9, I9, K9, M9, O9, Q9, S9, U9, W9, Y9, DA, FA, HA, JA, LA, NA, PA, RA, TA, VA, XA, ZA, cA, eA, gA, iA, kA, mA, PB, RB, TB, VB, YB, aB, cB, eB, gB, iB, kB, mB, KC, BD, DD, FD, HD, JD, LD, ND, PD, RD, TD, VD, XD, BE, DE, FE, HE, JE, LE, NE, PE, RE, TE, VE, XE, ZE, bE, dE, fE, hE, jE, lE, nE, pE, rE, tE, vE, PF, RF, TF, VF, YF, aF, cF, eF, gF, iF, kF, mF, BG, DG, FG, HG, JG, LG, NG, PG, RG, TG, VG, XG, ZG, bG, dG, fG, hG, jG, lG, nG, pG, rG, tG, vG, PI, RI, TI, VI, YI, aI, cI, eI, gI, iI, kI, mI, CJ, EJ, GJ, IJ, KJ, MJ, OJ, QJ, SJ, UJ, WJ, YJ | B-phycoerythrin beta chain | protein | 177 | 42% helix, 0% strand | P11393 |
| M1, 21, M4, 24 | LR7 | protein | 238 | 40% helix, 0% strand | — |
| Z1, a1, Z4, a4, A5, B5, C5, F5, G5, H5, L5, AC, BC, CC, FC, GC, HC, LC | B-phycoerythrin beta chain | protein | 146 | 64% helix, 0% strand | P11393 |
| b1, b4 | LR2_Hb | protein | 323 | 33% helix, 3% strand | — |
| o1, o4 | LR2_Hb | protein | 212 | 27% helix, 0% strand | — |
| 31, 34 | LR9 | protein | 285 | 26% helix, 12% strand | — |
| X2, X6, X7, XB, XF, XI | LR1 | protein | 324 | 35% helix, 5% strand | — |
| A2, A6, A7, AB, AF, AI | LR4 | protein | 257 | 51% helix, 0% strand | — |
| B2, BI | Phycobilisome rod-core linker polypeptide | protein | 230 | 43% helix, 1% strand | W0RZ90 |
| C2, E2, G2, I2, K2, M2, C6, E6, G6, I6, K6, M6, C7, E7, G7, I7, K7, M7, CB, EB, GB, IB, KB, MB, CF, EF, GF, IF, KF, MF, CI, EI, GI, II, KI, MI | C-phycocyanin alpha subunit | protein | 162 | 74% helix, 0% strand | W0RYI4 |
| D2, F2, H2, J2, L2, N2, D6, F6, H6, J6, L6, N6, D7, F7, H7, J7, L7, N7, DB, FB, HB, JB, LB, NB, DF, FF, HF, JF, LF, NF, DI, FI, HI, JI, LI, NI | C-phycocyanin beta subunit | protein | 172 | 73% helix, 0% strand | W0RZB2 |
| e3, eD | LR2 | protein | 248 | 39% helix, 2% strand | — |
| Y3, YD | LR4 | protein | 237 | 30% helix, 0% strand | — |
| B6, BB | Phycobilisome rod-core linker polypeptide | protein | 231 | 40% helix, 1% strand | W0RZ90 |
| B7, BF | Phycobilisome rod-core linker polypeptide | protein | 227 | 39% helix, 1% strand | W0RZ90 |
| b8, bA | LRC2 | protein | 380 | 43% helix, 2% strand | — |
| A8, AA, wE, xE, wG, xG | LR5 | protein | 238 | 56% helix, 0% strand | — |
| B8, BA, yE, yG | LR8 | protein | 250 | 63% helix, 1% strand | — |
| d9, dJ | LR3 | protein | 285 | 34% helix, 2% strand | — |
| A9, AJ | LR4 | protein | 256 | 32% helix, 0% strand | — |
| IC | B-phycoerythrin beta chain | protein | 176 | 52% helix, 0% strand | P11393 |
| zE, zG | LRC3 | protein | 370 | 46% helix, 1% strand | — |
| AH, CH, EH, GH, JH, KH, NH, PH, RH, TH, cH, eH, gH, iH, lH, mH, pH, rH, tH, vH | Allophycocyanin alpha subunit | protein | 160 | 73% helix, 0% strand | W0RYM0 |
| DH, FH, BH, HH, IH, LH, MH, OH, QH, SH, UH, dH, fH, hH, jH, kH, nH, oH, qH, sH, uH, wH | Allophycocyanin beta subunit | protein | 161 | 78% helix, 0% strand | W0S279 |
| VH, xH | Allophycocyanin gamma subunit | protein | 160 | 74% helix, 0% strand | W0S1U6 |
| WH, yH | Allophycocyanin beta 18 subunit | protein | 173 | 75% helix, 0% strand | W0RZE2 |
| XH, zH | Lc | protein | 92 | 18% helix, 23% strand | — |
| YH, 1H | Phycobilisome linker polypeptide | protein | 844 | 50% helix, 2% strand | W0RZJ2 |
| ZH, 2H | LRC4 | protein | 132 | 27% helix, 2% strand | — |
| aH, 3H | LRC5 | protein | 253 | 24% helix, 3% strand | — |
| bH, 4H | LRC6 | protein | 206 | 31% helix, 17% strand | — |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 1430 copies · chains A1, J1, B1, M1, C1, H1, D1, E1, F1, G1, L1, CD, I1, K1, KG, N1, W1, P1, Q1, O1, b1, C9, U1, R1, T1, S1, Z1, Y1, V1, X1, YH, aH, a1, c1, l1, e1, f1, d1, j1, o1, g1, i1, h1, n1, k1, m1, p1, y1, q1, 21, r1, w1, s1, t1, u1, v1, f2, 11, x1, z1, A2, l2, j2, C2, D2, M2, E2, F2, K2, G2, H2, I2, J2, M8, L2, N2, O2, Y2, X2, P2, Q2, e2, V2, FF, PF, R2, S2, 34, T2, U2, i2, a2, W2, Z2, O6, eD, b2, k2, c2, d2, g2, h2, m2, e3, WI, A3, J3, B3, Y3, C3, H3, G4, D3, E3, F3, G3, L3, P4, I3, K3, M3, V3, N3, O3, T3, lA, P3, Q3, R3, S3, X3, 31, U3, LJ, W3, HC, A4, J4, B4, M4, C4, H4, D4, E4, F4, L4, I4, K4, KE, N4, W4, Q4, O4, b4, CJ, U4, R4, T4, S4, Z4, Y4, V4, X4, 1H, 3H, a4, c4, l4, e4, f4, d4, j4, o4, g4, i4, h4, n4, k4, m4, p4, y4, q4, 24, r4, w4, s4, t4, u4, v4, fI, 14, dA, x4, z4, OA, A5, B5, CB, DB, C5, F5, G5, H5, I5, bA, 4H, JA, NA, J5, ZH, K5, L5, A6, b6, k6, C6, D6, M6, gE, B6, G6, I6, J6, H6, E6, F6, K6, L6, N6, Y6, Q6, R6, X6, P6, V6, BC, c6, S6, U6, T6, d9, a6, g6, W6, E9, Z6, d6, i6, e6, f6, h6, m6, j6, l6, A7, c7, f7, h7, C7, D7, M7, E7, F7, K7, G7, H7, I7, J7, L7, N7, O7, Y7, Q7, R7, X7, P7, V7, S7, U7, T7, a7, g7, W7, Z7, b7, k7, d7, e7, i7, m7, j7, l7, A8, d8, B8, C8, L8, E8, F8, D8, J8, b8, G8, I8, H8, N8, K8, bH, O8, X8, Q8, R8, P8, V8, S8, U8, T8, Z8, W8, Y8, a8, k8, e8, c8, i8, f8, h8, g8, m8, j8, l8, A9, T9, Y9, R9, B9, K9, D9, I9, F9, H9, G9, U9, M9, J9, L9, N9, W9, P9, Q9, O9, S9, V9, X9, AA, BA, CA, LA, AC, EA, FA, DA, GA, IA, HA, KA, MA, XA, QA, RA, PA, VA, SA, UA, TA, ZA, WA, YA, VI, SI, aA, kA, eA, cA, iA, fA, hA, gA, mA, jA, AB, bB, kB, MB, gG, BB, GB, IB, JB, KI, HB, EB, FB, KB, LB, NB, OB, YB, QB, RB, XB, PB, VB, cB, SB, UB, TB, dJ, aB, WB, EJ, ZB, dB, iB, eB, fB, hB, gB, mB, jB, FC, lB, CC, GC, IC, JC, 2H, KC, LC, AD, JD, BD, YD, HD, DD, ED, FD, GD, LD, ID, KD, MD, VD, ND, OD, TD, PD, QD, RD, SD, XD, UD, WD, AE, JE, BE, zE, CE, HE, DE, EE, FE, yE, TE, GE, LE, EH, IE, XE, ME, VE, OE, PE, NE, bE, QE, SE, RE, UE, WE, wE, YE, hE, aE, ZE, fE, iE, cE, KF, eE, dE, rE, jE, xE, kE, tE, mE, nE, lE, uE, oE, qE, pE, vE, sE, AF, cF, fF, hF, CF, DF, MF, EF, GF, HF, IF, JF, LF, NF, OF, YF, QF, RF, XF, VF, SF, TF, UF, aF, gF, WF, ZF, bF, kF, dF, eF, iF, mF, jF, lF, AG, JG, BG, zG, CG, HG, DG, EG, FG, yG, TG, GG, LG, gH, IG, XG, MG, VG, OG, PG, NG, bG, QG, SG, RG, UG, wG, WG, YG, hG, aG, ZG, fG, cG, eG, dG, rG, jG, iG, xG, kG, tG, mG, nG, lG, oG, qG, pG, vG, sG, uG, AI, lI, jI, CI, DI, MI, EI, FI, GI, HI, II, JI, LI, NI, OI, YI, XI, PI, QI, eI, RI, TI, UI, iI, aI, ZI, bI, kI, cI, dI, gI, hI, mI, AJ, TJ, RJ, OJ, BJ, KJ, DJ, IJ, FJ, GJ, UJ, HJ, MJ, JJ, NJ, WJ, PJ, QJ, SJ, YJ, VJ, XJ
- CYC · Phycocyanobilin · ligand · 120 copies · chains C2, F2, X2, D2, E2, H2, B2, G2, I2, L2, J2, K2, N2, M2, B6, J6, N6, C6, F6, X6, D6, E6, H6, G6, I6, L6, K6, M6, C7, F7, X7, D7, E7, H7, G7, B7, I7, L7, J7, M7, K7, N7, BB, JB, CB, FB, XB, DB, EB, HB, GB, IB, LB, KB, NB, MB, CF, FF, XF, DF, GF, EF, HF, BF, IF, LF, JF, MF, KF, NF, AH, FH, CH, BH, YH, DH, EH, GH, IH, HH, JH, b8, KH, MH, LH, XH, bH, zG, NH, OH, PH, SH, QH, RH, UH, TH, 3H, ZH, VH, WH, cH, fH, dH, 1H, eH, hH, gH, iH, kH, jH, lH, bA, mH, oH, nH, zH, 4H, zE, pH, qH, xH, rH, uH, sH, tH, wH, aH, vH, BI, 2H, yH, CI, FI, XI, DI, EI, HI, GI, II, LI, JI, KI, NI, MI
- PUB · Phycourobilin · ligand · 48 copies · chains A1, C1, M1, I1, K1, x1, z1, 21, p1, r1, A2, f2, h2, b2, d2, I3, K3, Y3, A3, C3, A4, C4, M4, I4, K4, x4, z4, 24, p4, r4, A6, f6, h6, j6, l6, A7, j7, l7, b7, d7, A8, j8, l8, f8, h8, B8, S8, U8, O8, Q8, A9, V9, X9, N9, P9, AA, jA, lA, fA, hA, BA, SA, UA, OA, QA, AB, fB, hB, jB, lB, ID, KD, YD, AD, CD, gE, iE, wE, YE, aE, xE, kE, mE, sE, uE, ME, OE, yE, UE, WE, AF, jF, lF, bF, dF, gG, iG, wG, YG, aG, xG, kG, mG, sG, uG, MG, OG, yG, UG, WG, AI, fI, hI, bI, dI, AJ, VJ, XJ, NJ, PJ
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.90 | 0.93 | 99 | CYC |
| 2 | 1095 | 0.90 | 0.92 | 99 | PEB |
| 3 | 2140 | 0.89 | 0.91 | 203 | PEB |
| 4 | 1587 | 0.89 | 0.91 | 149 | CYC |
| 5 | 3384 | 0.89 | 0.91 | 266 | CYC |
Interfaces
3,011 interfaces between chains.
- HH–YH · 2550 Ų buried · 23 hydrogen bonds · protein-protein
- jH–1H · 2539 Ų buried · 23 hydrogen bonds · protein-protein
- b8–F8 · 1915 Ų buried · 18 hydrogen bonds · protein-protein
- bA–FA · 1901 Ų buried · 19 hydrogen bonds · protein-protein
- JB–aH · 1857 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4550 cofactor, 332 modified, 107 covalent (phycoerythrobilin attachment, nonstandard, phycocyanobilin attachment, covalent ligand).
Compared structures
- P11393 · AlphaFold monomer V2.0 prediction for B-phycoerythrin beta chain (P11393) · a predicted model of the same protein · chain Z1 against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt E2IH77
- Every structure of UniProt P11393
- Every structure of UniProt W0RZ90
- Every structure of UniProt W0RYI4
- Every structure of UniProt W0RZB2
- Every structure of UniProt W0RYM0
- Every structure of UniProt W0S279
- Every structure of UniProt W0S1U6
- Every structure of UniProt W0RZE2
- Every structure of UniProt W0RZJ2
- Elsewhere: RCSB PDB 6KGX · PDBe 6KGX · UniProt E2IH77 · UniProt P11393 · UniProt W0RZ90 · UniProt W0RYI4 · UniProt W0RZB2 · UniProt W0RYM0 · UniProt W0S279 · UniProt W0S1U6 · UniProt W0RZE2 · UniProt W0RZJ2
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