2KODA

A high-resolution nmr structure of the dimeric c-terminal domain of hiv-1 ca
Total Genus 21
Loading diagram...

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
21
sequence length
88
structure length
88
Chain Sequence
MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVL
Loading diagram...

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

publication title Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
pubmed doi rcsb
source organism Hiv-1 m:b_hxb2r
molecule tags Viral protein
molecule keywords HIV-1 CA C-terminal domain
total genus 21
structure length 88
sequence length 88
chains with identical sequence B
ec nomenclature ec 2.7.7.49: RNA-directed DNA polymerase.
pdb deposition date 2009-09-18
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A 2kodA00
3DS1A 3DTJA 3DS3A 3DS0A 3NTEA 2M8LA 2XV6A 1A43A 5I4TG 5JPAA 2XXMA 3G28A 2BUOA 3LRYA 3VRLC 3DS4A 2KODA 4WYMA 4XFZA 2M8PA 5HGOA 2LF4A 3G1GA 4COCA 1AUMA 1D1DA 1EOQA 2JO0A 4U0AA 1A8OA 3MGEA 3P05A 1E6JP 4U0BA 3G29A 4XROA 1EIAA 3G21A 2JYGA 4COPA 4IPYA 3G0VA 3H47A 3G1IA 4M0IA 4PH1A 4U0FA 3DS5A 4U0EA 4XRQA 4U0CA 5DCKA 5HGLA 3G26A 5HGMA 1QRJA 2XT1A 2L6EA 2JYLA 2EIAA 2ONTA 4U0DA 3H4EA 4PH0A 5HGNA 4XFYA 4QNBA 4XFXA 1BAJA 2M8NA 3DS2A 3DPHA
chains in the Genus database with same CATH superfamily
1JJ2O 2LPKA 2LIWA 1QVGO 1YI2P 2KOOA 3NY7B 4WYMA 2KGAA 2KOPA 1S72P 2GZEA 3GZLA 2KR5A 2AVAA 2N98A 2DNWA 2XZ1C 2MVUA 1Q82Q 1T8KA 3CC7P 2PEMA 3Q20A 3LRYA 2BUOA 1GXGA 2ERHA 4U0BA 4XROA 1W2BO 3CE7A 2FQ0A 2MF4A 1YIJP 3EJEA 2FQ1A 3NTEA 2GYKA 1N8RQ 1Q7YQ 4BPHA 2K0YA 2M8PA 2KG6A 2BHVA 1VQPP 4HKGA 1ACPA 2VSQA 3H47A 4F37A 3EJBA 2EFJA 3HZQA 2KOSA 4QKOA 5HGNA 5EW5E 3CCRP 4XFXA 5HV8A 1YJWP 2E1MA 1VQMP 1NQ4A 1K73Q 1MZ8A 3DS4A 4IZ6A 2CGQA 2GDWA 2N5HA 3LMOA 4BPGA 4U0AA 1X3OA 2FVFA 1BXIA 3GJNA 3DS5A 1VQLP 2QEXP 2DGYA 1Z6MA 2OARA 4U0DA 1VKUA 1DNYA 2K93A 2Z44A 5F2OA 3M1MA 2OTLP 2PNGA 3GKLC 2AFDA 2LKIA 4XFZA 1D1DA 3CCSP 2KWLA 5HVCA 4GR6A 1EIAA 2JU1A 3G1IA 4U0FA 2MR8A 1Q81Q 2KORA 3CCMP 4U0CA 1VQ6P 2MVVA 3CCLP 2PEJA 2ONTA 3H4EA 1AF8A 2XV6A 2PEIA 2JQ4A 3CC2P 1YHQP 4NEOA 4R0MA 2K5XA 5KP8B 1L0IA 2JYGA 4PH1A 3CD6P 2KGCA 1KC8Q 2FQ2A 2KG8A 2MR7A 3CMAP 2FVAA 1HY8A 2K2QA 5F2NA 2FACA 3G6EP 2JGPA 3DPHA 1L0HA 3DS3A 2FVEA 3G28A 2LOLA 3P05A 3CCEP 2L9FA 4COPA 2JB0A 1E0HA 2P9XA 1VQ8P 2LL8A 1RO2A 2PEKA 1K8AQ 4GR2A 3DS0A 2JU2A 3HYBA 3G1GA 1EOQA 2JO0A 2PY8A 3CPWO 2GDYA 3CCJP 1M74A 3EJDA 1NJIQ 2QA4P 2K92A 2FAEA 4QNBA 2M8NA 1F80D 2ROQA 2XXMA 3B5IA 3WBHA 2M5RA 5HGOA 1A8OA 4PXHB 3G29A 3GZMA 1QVFO 2N5IA 5EJDA 4UHPB 1UNKA 4PH0A 4MRTC 2GZJA 2EG5A 1IUQA 5I4TG 2K0DX 2PEQA 1UJZA 2Z46A 5KP7B 3CCVP 1E6JP 3G21A 1YJNP 2CNRA 1IMQA 3OW2O 1AYIA 3CXCO 5HGMA 1RO0A 2KGDA 2VLNA 1YJ9P 3DS2A 2M8LA 2XZ0D 3DTJA 2N6ZA 3G4SP 2N6YA 1VQNP 5BS1A 2LIUA 1FR2A 3CMEP 3G0VA 1RNIA 3E2DA 5DCKA 2MD9A 1M6NA 2X2BA 4PWVB 4BPFA 1K30A 2L6EA 2KGEA 1VQ9P 2L22A 1KLPA 2CG5B 5CZDB 2PEOA 2KODA 3RG6C 1AUMA 2L4BA 2CQ8A 1KQSO 2VLPA 1VQOP 3RG2A 4IPYA 3B4QA 4XRQA 1DV5A 1ZNVA 1IMPA 1QRJA 2XT1A 1KD1Q 1BAJA 2VLQA 1Q86Q 4COCA 1CEIA 2FADA 1K9MQ 3MGEA 1VQ7P 1VQ5P 2KOQA 2QNWA 4DG9A 4M0IA 4U0EA 2L0QA 3CCUP 2Z45A 2OTJP 3I56P 5HGLA 2GZGA 1HQBA 7CEIA 1M1KQ 5BS2A 2EHSA 3DS1A 3U43A 2LTEA 2FHSC 3CCQP 2KW2A 3VRLC 1YITP 3H0DA 2AF8A 2NO8A 1GPJA 4CA3A 1GXHA 1VHNA 4H2YC 2EIAA 2K94A 5KP6B 1OR5A 2LMLA 2LF4A 4H2WC 2EHTA 1VQ4P 1VQKP 4H2XC 3G26A 2JBGA 1M90Q 2PENA 1ZMBA 2MY5A 2K0XA 1A43A 3G71P 2WPTA 1M6EX 5F2KA 2GDXA 1EMVA 5JPAA 3I55P 2VLOA 2N50A 2GZIA 2AFEA 2GZFA 3CC4P 2JYLA 2KG9A 4XFYA 2JAZA 2CWOA
chains in the Genus database with same CATH topology
1JJ2O 5F2OA 3M1MA 2OTLP 2XXMA 3B5IA 3WBHA 1QVGO 1YI2P 4WYMA 4XFZA 5HGOA 1Q86Q 4COCA 3CCSP 1D1DA 1S72P 1A8OA 3MGEA 1K9MQ 1VQ7P 1VQ5P 4GR6A 3G29A 1EIAA 1QVFO 3G1IA 4M0IA 4U0FA 1Q81Q 4U0EA 3CCMP 3CCUP 4U0CA 1VQ6P 2Z45A 2OTJP 3CCLP 3I56P 5HGLA 2PEJA 2ONTA 3H4EA 4PH0A 1Q82Q 1M1KQ 3CC7P 5BS2A 2EG5A 3DS1A 1IUQA 2PEMA 3Q20A 2XV6A 3CCQP 5I4TG 3LRYA 2BUOA 2PEQA 2PEIA 3VRLC 3CC2P 1YHQP 1YITP 3H0DA 2Z46A 3CCVP 1E6JP 4U0BA 4XROA 3G21A 1W2BO 2JYGA 4PH1A 3CD6P 1YJNP 1KC8Q 3OW2O 3CMAP 3CXCO 5HGMA 2EIAA 1YIJP 1RO0A 5F2NA 1YJ9P 3DS2A 2M8LA 3G6EP 3DPHA 3DTJA 3DS3A 3NTEA 3G28A 1N8RQ 3G4SP 1Q7YQ 2M8PA 2LF4A 2BHVA 5BS1A 1VQNP 3P05A 1VQPP 3CCEP 4COPA 3CMEP 3G0VA 3H47A 1VQ4P 1RNIA 1VQKP 2P9XA 3E2DA 5DCKA 1VQ8P 2EFJA 3HZQA 1M6NA 1RO2A 1K30A 3G26A 2L6EA 5HGNA 2PEKA 1VQ9P 1M90Q 3CCRP 4XFXA 2PENA 1K8AQ 1ZMBA 4GR2A 3DS0A 1YJWP 2E1MA 1VQMP 3HYBA 1A43A 1K73Q 2PEOA 3DS4A 2KODA 3RG6C 3G71P 1M6EX 3G1GA 5F2KA 1AUMA 1EOQA 2JO0A 4U0AA 1KQSO 2PY8A 1VQOP 5JPAA 3I55P 3CPWO 3CCJP 4IPYA 1M74A 3DS5A 4XRQA 1VQLP 2QEXP 1NJIQ 2DGYA 2OARA 3CC4P 1QRJA 2XT1A 2JYLA 4U0DA 2QA4P 1KD1Q 4XFYA 4QNBA 1BAJA 2M8NA 2CWOA 2Z44A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3DS1 A;  3DTJ A;  3DS3 A;  3DS0 A;  3NTE A;  2M8L A;  2XV6 A;  1A43 A;  5I4T G;  5JPA A;  2XXM A;  3G28 A;  2BUO A;  3LRY A;  3VRL C;  3DS4 A;  2KOD A;  4WYM A;  4XFZ A;  2M8P A;  5HGO A;  2LF4 A;  3G1G A;  4COC A;  1AUM A;  1D1D A;  1EOQ A;  2JO0 A;  4U0A A;  1A8O A;  3MGE A;  3P05 A;  1E6J P;  4U0B A;  3G29 A;  4XRO A;  1EIA A;  3G21 A;  2JYG A;  4COP A;  4IPY A;  3G0V A;  3H47 A;  3G1I A;  4M0I A;  4PH1 A;  4U0F A;  3DS5 A;  4U0E A;  4XRQ A;  4U0C A;  5DCK A;  5HGL A;  3G26 A;  5HGM A;  1QRJ A;  2XT1 A;  2L6E A;  2JYL A;  2EIA A;  2ONT A;  4U0D A;  3H4E A;  4PH0 A;  5HGN A;  4XFY A;  4QNB A;  4XFX A;  1BAJ A;  2M8N A;  3DS2 A;  3DPH A; 
#chains in the Genus database with same CATH topology
 1JJ2 O;  2LPK A;  2LIW A;  1QVG O;  1YI2 P;  2KOO A;  3NY7 B;  4WYM A;  2KGA A;  2KOP A;  1S72 P;  2GZE A;  3GZL A;  2KR5 A;  2AVA A;  2N98 A;  2DNW A;  2XZ1 C;  2MVU A;  1Q82 Q;  1T8K A;  3CC7 P;  2PEM A;  3Q20 A;  3LRY A;  2BUO A;  1GXG A;  2ERH A;  4U0B A;  4XRO A;  1W2B O;  3CE7 A;  2FQ0 A;  2MF4 A;  1YIJ P;  3EJE A;  2FQ1 A;  3NTE A;  2GYK A;  1N8R Q;  1Q7Y Q;  4BPH A;  2K0Y A;  2M8P A;  2KG6 A;  2BHV A;  1VQP P;  4HKG A;  1ACP A;  2VSQ A;  3H47 A;  4F37 A;  3EJB A;  2EFJ A;  3HZQ A;  2KOS A;  4QKO A;  5HGN A;  5EW5 E;  3CCR P;  4XFX A;  5HV8 A;  1YJW P;  2E1M A;  1VQM P;  1NQ4 A;  1K73 Q;  1MZ8 A;  3DS4 A;  4IZ6 A;  2CGQ A;  2GDW A;  2N5H A;  3LMO A;  4BPG A;  4U0A A;  1X3O A;  2FVF A;  1BXI A;  3GJN A;  3DS5 A;  1VQL P;  2QEX P;  2DGY A;  1Z6M A;  2OAR A;  4U0D A;  1VKU A;  1DNY A;  2K93 A;  2Z44 A;  5F2O A;  3M1M A;  2OTL P;  2PNG A;  3GKL C;  2AFD A;  2LKI A;  4XFZ A;  1D1D A;  3CCS P;  2KWL A;  5HVC A;  4GR6 A;  1EIA A;  2JU1 A;  3G1I A;  4U0F A;  2MR8 A;  1Q81 Q;  2KOR A;  3CCM P;  4U0C A;  1VQ6 P;  2MVV A;  3CCL P;  2PEJ A;  2ONT A;  3H4E A;  1AF8 A;  2XV6 A;  2PEI A;  2JQ4 A;  3CC2 P;  1YHQ P;  4NEO A;  4R0M A;  2K5X A;  5KP8 B;  1L0I A;  2JYG A;  4PH1 A;  3CD6 P;  2KGC A;  1KC8 Q;  2FQ2 A;  2KG8 A;  2MR7 A;  3CMA P;  2FVA A;  1HY8 A;  2K2Q A;  5F2N A;  2FAC A;  3G6E P;  2JGP A;  3DPH A;  1L0H A;  3DS3 A;  2FVE A;  3G28 A;  2LOL A;  3P05 A;  3CCE P;  2L9F A;  4COP A;  2JB0 A;  1E0H A;  2P9X A;  1VQ8 P;  2LL8 A;  1RO2 A;  2PEK A;  1K8A Q;  4GR2 A;  3DS0 A;  2JU2 A;  3HYB A;  3G1G A;  1EOQ A;  2JO0 A;  2PY8 A;  3CPW O;  2GDY A;  3CCJ P;  1M74 A;  3EJD A;  1NJI Q;  2QA4 P;  2K92 A;  2FAE A;  4QNB A;  2M8N A;  1F80 D;  2ROQ A;  2XXM A;  3B5I A;  3WBH A;  2M5R A;  5HGO A;  1A8O A;  4PXH B;  3G29 A;  3GZM A;  1QVF O;  2N5I A;  5EJD A;  4UHP B;  1UNK A;  4PH0 A;  4MRT C;  2GZJ A;  2EG5 A;  1IUQ A;  5I4T G;  2K0D X;  2PEQ A;  1UJZ A;  2Z46 A;  5KP7 B;  3CCV P;  1E6J P;  3G21 A;  1YJN P;  2CNR A;  1IMQ A;  3OW2 O;  1AYI A;  3CXC O;  5HGM A;  1RO0 A;  2KGD A;  2VLN A;  1YJ9 P;  3DS2 A;  2M8L A;  2XZ0 D;  3DTJ A;  2N6Z A;  3G4S P;  2N6Y A;  1VQN P;  5BS1 A;  2LIU A;  1FR2 A;  3CME P;  3G0V A;  1RNI A;  3E2D A;  5DCK A;  2MD9 A;  1M6N A;  2X2B A;  4PWV B;  4BPF A;  1K30 A;  2L6E A;  2KGE A;  1VQ9 P;  2L22 A;  1KLP A;  2CG5 B;  5CZD B;  2PEO A;  2KOD A;  3RG6 C;  1AUM A;  2L4B A;  2CQ8 A;  1KQS O;  2VLP A;  1VQO P;  3RG2 A;  4IPY A;  3B4Q A;  4XRQ A;  1DV5 A;  1ZNV A;  1IMP A;  1QRJ A;  2XT1 A;  1KD1 Q;  1BAJ A;  2VLQ A;  1Q86 Q;  4COC A;  1CEI A;  2FAD A;  1K9M Q;  3MGE A;  1VQ7 P;  1VQ5 P;  2KOQ A;  2QNW A;  4DG9 A;  4M0I A;  4U0E A;  2L0Q A;  3CCU P;  2Z45 A;  2OTJ P;  3I56 P;  5HGL A;  2GZG A;  1HQB A;  7CEI A;  1M1K Q;  5BS2 A;  2EHS A;  3DS1 A;  3U43 A;  2LTE A;  2FHS C;  3CCQ P;  2KW2 A;  3VRL C;  1YIT P;  3H0D A;  2AF8 A;  2NO8 A;  1GPJ A;  4CA3 A;  1GXH A;  1VHN A;  4H2Y C;  2EIA A;  2K94 A;  5KP6 B;  1OR5 A;  2LML A;  2LF4 A;  4H2W C;  2EHT A;  1VQ4 P;  1VQK P;  4H2X C;  3G26 A;  2JBG A;  1M90 Q;  2PEN A;  1ZMB A;  2MY5 A;  2K0X A;  1A43 A;  3G71 P;  2WPT A;  1M6E X;  5F2K A;  2GDX A;  1EMV A;  5JPA A;  3I55 P;  2VLO A;  2N50 A;  2GZI A;  2AFE A;  2GZF A;  3CC4 P;  2JYL A;  2KG9 A;  4XFY A;  2JAZ A;  2CWO A; 
#chains in the Genus database with same CATH homology
 1JJ2 O;  5F2O A;  3M1M A;  2OTL P;  2XXM A;  3B5I A;  3WBH A;  1QVG O;  1YI2 P;  4WYM A;  4XFZ A;  5HGO A;  1Q86 Q;  4COC A;  3CCS P;  1D1D A;  1S72 P;  1A8O A;  3MGE A;  1K9M Q;  1VQ7 P;  1VQ5 P;  4GR6 A;  3G29 A;  1EIA A;  1QVF O;  3G1I A;  4M0I A;  4U0F A;  1Q81 Q;  4U0E A;  3CCM P;  3CCU P;  4U0C A;  1VQ6 P;  2Z45 A;  2OTJ P;  3CCL P;  3I56 P;  5HGL A;  2PEJ A;  2ONT A;  3H4E A;  4PH0 A;  1Q82 Q;  1M1K Q;  3CC7 P;  5BS2 A;  2EG5 A;  3DS1 A;  1IUQ A;  2PEM A;  3Q20 A;  2XV6 A;  3CCQ P;  5I4T G;  3LRY A;  2BUO A;  2PEQ A;  2PEI A;  3VRL C;  3CC2 P;  1YHQ P;  1YIT P;  3H0D A;  2Z46 A;  3CCV P;  1E6J P;  4U0B A;  4XRO A;  3G21 A;  1W2B O;  2JYG A;  4PH1 A;  3CD6 P;  1YJN P;  1KC8 Q;  3OW2 O;  3CMA P;  3CXC O;  5HGM A;  2EIA A;  1YIJ P;  1RO0 A;  5F2N A;  1YJ9 P;  3DS2 A;  2M8L A;  3G6E P;  3DPH A;  3DTJ A;  3DS3 A;  3NTE A;  3G28 A;  1N8R Q;  3G4S P;  1Q7Y Q;  2M8P A;  2LF4 A;  2BHV A;  5BS1 A;  1VQN P;  3P05 A;  1VQP P;  3CCE P;  4COP A;  3CME P;  3G0V A;  3H47 A;  1VQ4 P;  1RNI A;  1VQK P;  2P9X A;  3E2D A;  5DCK A;  1VQ8 P;  2EFJ A;  3HZQ A;  1M6N A;  1RO2 A;  1K30 A;  3G26 A;  2L6E A;  5HGN A;  2PEK A;  1VQ9 P;  1M90 Q;  3CCR P;  4XFX A;  2PEN A;  1K8A Q;  1ZMB A;  4GR2 A;  3DS0 A;  1YJW P;  2E1M A;  1VQM P;  3HYB A;  1A43 A;  1K73 Q;  2PEO A;  3DS4 A;  2KOD A;  3RG6 C;  3G71 P;  1M6E X;  3G1G A;  5F2K A;  1AUM A;  1EOQ A;  2JO0 A;  4U0A A;  1KQS O;  2PY8 A;  1VQO P;  5JPA A;  3I55 P;  3CPW O;  3CCJ P;  4IPY A;  1M74 A;  3DS5 A;  4XRQ A;  1VQL P;  2QEX P;  1NJI Q;  2DGY A;  2OAR A;  3CC4 P;  1QRJ A;  2XT1 A;  2JYL A;  4U0D A;  2QA4 P;  1KD1 Q;  4XFY A;  4QNB A;  1BAJ A;  2M8N A;  2CWO A;  2Z44 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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